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The Head of the Atlantis Expedition and Her Ranking Military Officer

Summary:

A collection of Stargate Atlantis one shots centering around Elizabeth Weir and John Sheppard--and how they are ridiculously in love with each other.

Chapter 1: "You Need to Forgive Yourself"

Summary:

John Sheppard reads Elizabeth Weir’s final goodbye.

Note: Takes place almost directly after the events of Season 4, Episode 10 “This Mortal Coil”. Canon compliant—Elizabeth and John are confirmed to be in love with each other, but nothing ever happens about it. All hurt, no comfort.

Notes:

(See the end of the chapter for notes.)

Chapter Text

Officially, Sheppard was checking the condition of the P-90s in weapons locker four. In reality, he was cleaning his own sidearm and hiding from the rest of his team. From the rest of the entire expedition, really. He was tired of the looks. Every time he walked into a room since they had gotten back from the world with the clones, everyone looked at him like he was about to break. He was tired of being someone who needed to be pitied.

And his own team was the worst. McKay didn’t know what to say and, as a result, said anything else that he could think of. Zelenka kept nodding sadly and patting him on the shoulder. Teyla repeatedly asked him if he “needed to talk”. Ronon was the only person who John could really stand to be around at the moment, but he was on the mainland.

So, his pistol was sitting completely deconstructed on a cargo crate and he had polished it until it shown. John had never been much for the spit-shine, buttoned up military traditions, but at least this gave him something to do with hands. And, as much as his mind felt like it was shattering apart, his hands didn’t shake.

John was half considering going back out into the city when he heard a soft knock at the door. He stifled a groan but walked over and swung it open anyways.

Teyla stood at the threshold, a small pile of cream-colored envelopes in her hand.

“Hello, John,” she said with a soft smile. He hated that smile.

“Teyla.”

She hesitated a moment, as if trying to figure out if he was going to invite her in. When he didn’t budge from the doorway, Teyla took a small step back with a quiet sigh. On some level, John knew he should move. He knew that letting her in and talking about things would probably help. But he was beginning to think that whatever progress he had made “letting people in” had died with Elizabeth.

“What can I do for you?” John said, breaking the silence and trying to pull back on the cocky, unbothered hotshot pilot mask. It didn’t seem to be fooling Teyla. She just took a moment to look at him intently before answering.

“When I was packing up Dr. Weir’s things a few months ago, I found letters she wrote to a few of the members of the expedition. They were meant to be shared in the event of her death. I have been delivering them,” she said, holding out one of the envelopes to him.

John really wanted to turn her away. He didn’t want to know what was in that letter. It made everything too real and too final. But this was Teyla and he respected her too much for that.

He reached out and took the envelope. It was made of a thick, textured cardstock. Of course Elizabeth had brought high quality stationary into an entirely new galaxy. He also noticed that his letter was by far the thinnest in the bunch.

“Thanks. And thanks for taking care of packing it all up,” he said. About a week after they had gotten back from the Replicator home world, Colonel Carter had asked him to do it. He had asked Teyla.

“I am glad I was able to help,” she said, giving him another smile. “John… if you need anything, you only have to ask.”

He glanced down, trying not to cringe. Teyla touched the side of his face gently, raising his head up so he had to meet her eyes.

“I mean it. You are not alone in this.”

“Thanks, Teyla. But I’m fine,” John insisted, patting her arm so she would stop touching him. Teyla didn’t look like she believed him, but she took the hint. She removed her hand and inclined her head, before giving him another smile and leaving. He shut the door behind her.

John looked at the letter in his hand. His full name and rank were written across the top, in Elizabeth’s small, precise handwriting. He almost opened it then and there. But there was an awful pressure building in his chest, so he shoved it in his back pocket. He put his sidearm back together and headed back to his room, ready to bury the letter in the bottom of a drawer and forget about it.

 

And for two weeks, John managed to put it out of his head. Based on what he could tell, most people had read their letters immediately. When he had met McKay and Teyla for dinner later in the mess, he noticed quite a few people with red eyes. The general noise was quieter and even Rodney seemed content with pushing his food around and not saying a word. Zelenka had started sniffling loudly and ended up leaving without finishing his meal.

It was after a particularly nasty visit to a new planet that John finally broke down and opened it. In the past, after a mission like that, Elizabeth would have found him on the pier with two glasses of whatever alcohol she could find. They would talk until they didn’t need to anymore and by the end John would have made her laugh enough that he’d end up feeling a bit better. A little more human and a little less broken.

Damn he missed her.

His hands were steady as he opened the envelope. A small photograph fell out first. He didn’t know who had taken it, but it was him and Elizabeth, leaning up against one of the railings. They each had a cup in their hands and Elizabeth’s head was thrown back with laughter. John had an answering smirk on his face. He carefully put the photograph on his nightstand before turning his attention to the letter.

John,

I couldn’t quite find the words to tell you what you mean to me. I guess I’m hoping, at least on some level, you already know.

Don’t lash out at whoever takes over this position after me. I know you are hurting, but it isn’t their fault. And they are going to need you. Atlantis is going to need you. It always has.

I’m sorry we couldn’t finish this adventure together. You certainly made every day something to remember. It is my sincerest hope that you continue to go out and fight to save this galaxy—and stay the man I know.

I don’t know how I died. But I have a feeling I need to say this—you need to forgive yourself. In the three years I have known you, I have never seen you give up on someone. This is not your fault. I knew the risks coming here. I chose to come, and I chose to stay, despite them. Respect that choice and don’t blame yourself.

One last thing. You are a good man, John Sheppard. Don’t let anyone—even yourself—try to convince you otherwise.

All my love,

Elizabeth

He let go of the letter after reading it and watched it float slowly to the ground. Alone in his room, in the middle of the night, John Sheppard found the strength to grieve.

Notes:

Quote prompt from the blog creativepromptsforwriting on tumblr.

I got inspired from the song "Not Dark Yet" by Calum Scott.

Chapter 2: Girl's Night

Summary:

Teyla Emmagan and Elizabeth Weir are having a girl’s night, complete with wine, gossip, and one drunken accidental confession about a certain top ranking military officer.

Note: Takes place a few weeks after the events of Season 2, Episode 8 “Conversion”. Canon compliant—Elizabeth is just confirmed to be in love with John, but nothing actually happens that would break canon, except for a very brief conversation in Season 5, Episode 5. Absolute fluff.

Chapter Text

“How are things going with Colonel Caldwell?” Teyla asked Elizabeth as she refilled both of their wine glasses.

Elizabeth took a sip of wine and rolled her eyes.

“It’s mostly fine. Now that John is up to visitors, Caldwell has been discussing any major decisions or changes with him. They’ve actually found some common ground. Not that either of them would admit it.”

Elizabeth had been in Teyla’s quarters for the last half hour and they were well on their way through a bottle of wine. A few months after their arrival in Atlantis, Teyla had invited her over just to spend time together. Elizabeth always felt there was a wall up between her and the people she commanded. One that certainly did not allow for draining a bottle or two of wine and gossiping. Teyla, as an Athosian on John’s team, was a grey area that Elizabeth could work with. They had been meeting at least monthly ever since.

“Of course not. It is far easier for them to continue disliking one another,” Teyla said with a knowing smile.

Elizabeth raised her glass in mock salute.

“Have you visited John recently?” Teyla asked, her tone overly casual. Elizabeth raised an eyebrow.

“I was there earlier today. He’s doing well. Most of the chitin is gone now. It still covers his right forearm, but it’s shrinking every day,” she answered, choosing to take her friend’s question at face value. “I think he still gets tired out faster than he’d like. But I think he’ll be back on duty in the next two or three weeks.”

John being frustrated with his energy levels was a little bit of an understatement. She’d come over in the late afternoon and he had looked almost completely drained. For a man who could usually run a few miles before feeling tired, being wiped out by just existing was getting to him. Though every time he bugged her about letting him return to active duty, it was nice to be able to point out he was propped up on pillows without the strength to sit up himself.

“I am glad to hear that he is doing well today. We are anxious to have him back with us. Though Major Lorne is doing a wonderful job,” she said.

Elizabeth inclined her head in acknowledgement of the compliment to Lorne. As eager as John was to get back out there, she could tell he was fiercely proud of how Major Lorne was handling things with AR-1. Teyla swirled her wine around in her glass, looking like she was contemplating bringing something up. Elizabeth just took another sip. She wasn’t going to pressure Teyla into talking about anything she didn’t want to. That’s not how girl’s night worked.

“Did I ever tell you about Colonel Sheppard’s… odd behavior just before we realized something was wrong?” Teyla asked, a mischievous smile on her face

“No, I don’t think you did,” Elizabeth replied. They both knew that Teyla hadn’t said anything. But this was part of getting Teyla to gossip.

“We were sparring in the gym. As we now know, his condition gave him increased strength and speed, as well as a… more agitated temperament than normal. During our fight, he was able to completely disarm me and pin me.”

Elizabeth was slightly impressed. She had caught a few of their sparring matches before. John had been improving, but he hardly ever came close to actually beating Teyla.

“Really? That’s a first,” she said.

Teyla nodded, hesitating a bit.

“Then he proceeded to ask me to call him John while we are off duty… and kiss me,” she finished.

Elizabeth almost choked on her wine. Teyla was laughing.

“He did what!?” Elizabeth finally sputtered out.

“Kissed me. In the middle of the gym. While pinning me up against the wall,” Teyla confirmed.

“Do you need me to make a report?” Elizabeth asked, though she was pretty sure she already knew the answer.

“I think we have established that John was hardly in control of his actions,” she answered. “And I do believe he feels awful about the entire situation. He keeps pretending to be asleep when I visit the infirmary.”

Now both women were laughing. Elizabeth couldn’t believe that Lieutenant Colonel John Sheppard, the man who would storm a wraith ship with nothing but a knife and pure spite, was faking sleep to avoid an awkward conversation. Though now that she thought about it, it made perfect sense.

After more laughing, the two women finally got their breath under control. Now it was Elizabeth’s to look down at her glass, trying to decide whether to ask the question she wanted to. It was going to put her in dangerous territory.

“Is there something you wish to ask me?” Teyla said, her voice charmingly neutral. Which meant she probably knew exactly what Elizabeth was going to ask.

“Well… how was it?”

Teyla busted out laughing again. Elizabeth felt herself blush.

“I don’t typically like being ummm… pinned against a wall, but…”

Elizabeth smiled at Teyla dramatically drawing out her answer. As she waited for her to finish, Elizabeth found herself thinking that she really wouldn’t mind being pinned up against a wall by John Sheppard.

Then she heard Teyla choke on her own wine. Elizabeth’s head snapped up. Teyla’s eyes were wide, but she was smiling.

“Please tell me I did not just say that out loud,” Elizabeth said, absolutely mortified. Teyla had to work with John. And Elizabeth had to work with John. They both had to work with the man she evidently wanted to pin her against a wall.

“You more… muttered it into your wine,” she answered, still grinning. “But we can pretend it never happened, if that is what you would like.” Teyla’s expression made it very clear that, while she would never bring it up again if that is what Elizabeth preferred, she would much rather talk about what Elizabeth just admitted. In detail.

Elizabeth gave a noncommittal shrug. Part of her wanted to act like it never happened. Because it could never happen. He reported to her. They had an uneven power dynamic in a myriad of ways and she was pretty sure they’d be breaking some sort of international law. But the other part wanted to talk to someone about this. She’d been dealing with it quietly ever since they had returned to earth. And if she was being honest with herself, she had probably been hiding from it a lot longer than that. Elizabeth had realized that on some level when had given him permission to take the nuke. Her chest had felt like it was going to break open watching him run up the stairs to the jumper bay.

“To answer your original question, John… knows what he is doing,” Teyla said. She smiled at Elizabeth again, knowing exactly what that would do to her. Elizabeth topped off her wine.

“How long have you known?” she finally asked.

“I did not know so much as suspect. There was something in the way you looked at each other after the siege. Like something had changed. At first, I thought it may just be the aftermath of adrenaline and battle. However, when you both returned from earth, it was still there. And then, after what happened with the retrovirus, the difference was even more pronounced.”

“And here I thought I was doing a good job hiding it,” Elizabeth responded with a small laugh.

“Why would you hide it?”

“It’s… complicated.”

Teyla refilled her wine glass. They were almost finished with the bottle.

“I understood before, when you were still engaged to Simon. I can see how that would be complicated,” Teyla started. “But now, why would you not be with him? It is clear he is just as in love with you as you are with him. If not more so.”

Elizabeth stared at her. That couldn’t be true. Because if it was true… that would make it so much more difficult to stay away from him.

“You can’t know that,” she said.

Teyla looked back at her and shifted so she was sitting closer to Elizabeth. The expression on her face was a mixture of understanding and pity.

“Elizabeth. When Colonel Sheppard was infected with the retrovirus, when he was losing who he was, he trusted you to end it. If it came to that. And John of all people knows what he was asking you to do, and what the cost would be. He trusted you to love him enough to kill him. And he trusted his love for you enough to know he wouldn’t resist if it meant hurting you. I do not know how anyone could doubt after that.”

Elizabeth looked at the ground. When Teyla put it that way, it felt alarmingly clear. She had tried so hard not to think of the day John asked her to kill him. The despair in his voice and the pleading in the eyes she no longer recognized. Elizabeth knew, that if it had come to that, if they had lost him completely, she would have done what he asked. Even if it destroyed her.

“We can’t. We would either have to keep it a secret or one of us would have to step down. I refuse to lie, and I can’t bring myself to leave my position here. I would never ask John to give up the one thing that has finally given him purpose. And although it’s a bit muddy, he reports to me. It could ruin everything and then I could lose him,” Elizabeth tried to explain. “I can’t risk that. If we stay just what we are, everything can keep going.”

“With what we do, and the risks Colonel Sheppard takes, you could lose him at any time. He could lose you. A future with those we love is never guaranteed. Would you not rather be honest?” Teyla asked earnestly.

Elizabeth thought about all the times she almost lost him. All those times she wondered if she was going to get to see him again. If the last time was the last time he would make her laugh when she wanted to scream. The last time she would get to see him grin and have to convince herself she couldn’t kiss him.

“I can’t.”

Teyla nodded, looking away. Elizabeth suddenly had the sneaking suspicion that this conversation wasn’t entirely about her and John.

“Teyla. Pot. Kettle,” she said, gesturing between the two of them.

“What do you mean?” the other woman asked, feigning ignorance at the earth idiom.

“You are clearly in love with a certain Athosian and have done nothing about it,” she said, feeling just a bit triumphant.

“Kanaan and I are… complicated,” Teyla said, reusing Elizabeth’s word.

“Ha! So it is Kanaan,” she said. “What is complicated about the two of you?”

Teyla was silent for a moment before grinning at her. Elizabeth suddenly felt like she had taken a risk she wasn’t aware of.

“Okay, Elizabeth. I will make you a bargain,” Teyla started. Elizabeth eyed her suspiciously. “I will tell Kanaan how I feel, if you are truthful with Colonel Sheppard.”

“What am I supposed to do, walk up to him, grab him by the jacket, and kiss him in the middle of the command tower?” she asked, exasperated. It was not the same situation. Not at all.

Teyla gave her a look. She may have been a bit too specific. Now Teyla knew that Elizabeth has had that exact fantasy. Multiple times.

“If that is what you wish to do, I certainly will not discourage you. But I do not believe that is what I would do, if I were you.”

“Oh, and what would you do?” Elizabeth was actually curious.

“You and Colonel Sheppard usually spend time with each other on one of the piers after a mission, do you not?”

She nodded. Elizabeth was pretty sure she would have lost her mind within the first month without those talks. Sometimes they talked about what went wrong on the mission. Sometimes they would talk about everything but.

“That is when I would tell him your true feelings. Alone, in a space that is just yours, and while the sun is setting over the horizon.”

Elizabeth raised an eyebrow at her, a grin she could no longer hide spreading across her face.

“Okay… that would be very romantic. I will give you that one.”

Both women spent a few minutes sitting in silence, sipping their wine. If Elizabeth had to guess, Teyla was thinking of Kanaan. She was definitely thinking about John.

“And… if you make the first move, I win a bet with Ronon,” Teyla said, putting on a shit eating grin that would’ve made John proud.

“Please tell me the entirety of Atlantis doesn’t have a betting pool going on whether John and I will get together,” Elizabeth said with a groan.

“The only bet I am aware of is between Ronon and myself,” she responded, leaving out the very clear implication that just because she didn’t know of any, didn’t mean there weren’t any.

“If anything ever does happen, I think you will win that bet.”

“You don’t think Colonel Sheppard would come to you first?”

“The last time I hugged Colonel Sheppard, he had to buffer for a full thirty seconds. Today I sat down on his hospital bed a full four inches away from his thigh and he still froze for a moment. I think he would spontaneously combust before initiating any meaningful physical contact, romantic or otherwise.”

Now they were both laughing again, and the conversation eventually veered off into other topics. After polishing off another bottle, they said goodbye and Elizabeth started the walk back to her own room. She was still mildly embarrassed that Teyla had seen right through all of her attempts to remain professional. But mostly, she just felt relieved to have finally admitted it to someone. Even if she never intended to do anything about it.

When Elizabeth got back to her room, she showered and stretched out across her bed with a smile on her face. And if she spent the moments before falling asleep thinking about John Sheppard pinning her against wall… well, that was no one’s business but her own.

Chapter 3: "You Make Me Feel Safe"

Summary:

AR-1 and Elizabeth Weir are caught in a tunnel collapse. Everyone is a bit beat up, but John ends up taking care of a concussed and overly honest Elizabeth until they can get out.

Note: In my head, this takes place sometime in season 3. But really it could be in either 2 or 3. Canon compliant. Mostly. Hurt/comfort.

Notes:

(See the end of the chapter for notes.)

Chapter Text

Sheppard was thrown backwards with the force of the explosion. He felt himself slam into the back of the cave and rolled to the floor. Everything hurt. After a moment of lying dazed, John managed to convince himself to sit up with a groan.

He was pretty sure his body was just one giant bruise, but his head felt fine, and nothing seemed broken. He’d take it. Using the offending cave wall to haul himself to his feet, John made the painful discovery that he hadn’t been entirely correct. He had at least one cracked or broken rib and when he touched his side, his fingertips came away bloody. Shit.

“Alright, sound off. Who’s dead?” Sheppard asked, his voice cracking a bit. His flashlight was miraculously intact. He had just flipped it on when he heard a grumble from his right.

“Still alive,” Ronon said, getting to his feet without too much difficulty.

John slowly swept the flashlight around the cave. The entire ceiling had collapsed down on them, blocking them from the exit. There was a body half buried in rubble. It looked like Rogers.

“Rodney? Dr. Weir?” he asked, walking closer to the cave in. It looked fairly stable.

“Sheppard! Are you alright? Is anyone dead?” Rodney’s voice could be heard on the other side of the rubble.

“Me and Ronon are fine. Rogers wasn’t so lucky. Who are you missing in your side?”

“Dr. Quora and Dr. Weir. Zelenka is here with me. He’s a bit shaken, but I’m fine,” came Rodney’s answer

“I am not sh—” Zelenka started, indignant.

“Shut up. Now is not the time. I’m—"

“Rodney!” Sheppard barked. “What happened?”

“Looks like someone planted low grade explosive devices in strategic places along the ceiling. They must have known we would have to come this way.”

“Any chance of getting us out of here?”

“I’m working on it,” McKay snapped.

“Well, work on it faster.”

“Sheppard,” Ronon said, his voice urgent. “You better get over here.”

“Keep me updated, Rodney,” Sheppard ordered. He thought he heard an annoyed muttering but couldn’t make out the words. That was fine with him.

He walked carefully over to the corner where Ronon was standing. Fallen rocks littered the cave floor, some jagged and the size of small boulders. Ronon had turned on his own light and when Sheppard finally navigated to him, he saw it was shining on a barely conscious Elizabeth Weir.

John kneeled down next to her, successfully ignoring the throb of pain from his ribcage. Her eyes were unfocused and there was a decent sized gash along her hairline.

“Dr. Weir, can you hear me?” he said, keeping his voice clear and even. His adrenaline was spiking through the roof, but there wasn’t time for that.

“John…” Elizabeth slurred out.

“There she is. Alright, don’t move. I’m going to shine my light into your eyes, and I need you to remain absolutely still,” Sheppard instructed. She gave a small nod of understanding. He decided to let that bit of movement slide.

Dr. Weir’s eyes did not react to the flashlight. Sheppard wasn’t exactly sure what that meant, but he was damn sure it wasn’t good.

“Ok, can you tell me where you are injured?” he asked.

Elizabeth blinked slowly, as if trying to focus.

“My head hurts. And I think there is something wrong with my leg,” she finally managed to get out.

John glanced down to her legs. There was a jagged cut along her right thigh, but it was only bleeding sluggishly. Nothing else seemed overly damaged.

“Ok, good, good. We’re going to lay you down flat so we can get a better look at you. It’s probably going to hurt but we’ll move quickly,” Sheppard said, his voice still flat and even. He stripped off his tac vest and jacket, clenching his teeth against the twinge in his ribs, and folded the jacket up into a makeshift pillow. Then he motioned to Ronon.

It took a few moments, and a sharp cry of pain from Dr. Weir, but they managed to get her lying flat with her head on his jacket.

“John! What was that?” Rodney called from the other side.

“We found Weir. She’s injured, but it doesn’t look like anything she can’t pull out of. We needed to get her into a safer position,” John answered.

“Any sign of Dr. Quora?”

“Nothing,” Ronon said. Sheppard heard McKay curse quietly.

“I’m going to see how stable the rubble is. Maybe we can get you out that way. Zelenka is going to see if he can get in contact with Atlantis.”

Sheppard didn’t like Zelenka going by himself, but there didn’t seem to be much choice.

“Alright, be careful,” he said. Rodney was muttering again. John ignored him and turned his attention back to Elizabeth.

“Dr. Weir, I’m going to bandage up that leg and then check you for any other injuries. You’re pretty banged up, so me touching you at all is going to hurt. But I need you to tell me if any of the pain is sharper or if it feels like something is tearing.”

“I’m ready,” she said, her voice soft.

Sheppard was barely aware of Ronon standing over him as he pulled a roll of bandages out of his tac vest and made quick work out of wrapping her leg. She cried out a bit at the applied pressure but managed not to move too much. John slid his hands over her body, checking for more blood. He put a bit of pressure on her stomach and back, but Elizabeth remained fairly still and quiet.

“It looks like it’s just your leg and your head. You’ll be fine in no time. Just stay awake for me,” John said, moving to get up.

Weir moved faster than he thought possible and grabbed him by the arm, stopping him in an awkward half stooped position. His ribs were screaming.

“Don’t go,” she said, slightly louder than before. Her eyes were wide, and she had a vice-like grip on his arm. Sheppard froze for a moment. Elizabeth looked terrified. He sat back down, trying to hide his wince. She laid her head down on his thigh, still holding on to his arm.

Sheppard glanced up to Ronon, slightly panicked. Ronon shrugged.

“I need to check in with Rodney. See when he’s getting us out of here,” John said, carefully trying to free his arm.

“Please don’t leave me.”

Dr. Weir must have hit her head harder than he thought.

“Sheppard! Are you there? I think I’ve got a plan,” Rodney yelled.

“Go ahead, McKay,” Sheppard yelled back, still sitting with Elizabeth.

“I think we’ve got a way to dig out the rubble enough for you to make it out. But I’m going to need someone on that side to help stabilize.”

“You stay here,” Ronon said gruffly. “You’re injured.”

John made a face as the larger man walked toward the rubble wall. And here he thought he had been hiding it so well.

“Ready, McKay,” Ronon said. Rodney started explaining the plan while Ronon made nondescript grunts of understanding.

Sheppard looked back down at Dr. Weir. She was watching Ronon at the wall. With a sigh, John began to shift his weight until he was leaning against a relatively flat boulder. He carefully repositioned Elizabeth, so she was more upright, leaning her against his chest. She seemed determined not to let go of his arm, so he just draped it over her. Something tightened in John’s chest when she snuggled deeper into him, her head nestled just under his chin.

“You can’t go to sleep, Elizabeth,” Sheppard said, studiously ignoring the part of him that just wanted to lean further in and pull her closer.

“Mmmhmm,” she murmured, turning her face farther into his chest. She was going to kill him at this rate.

“I mean it. You’re going to die on my watch and then the I.O.A. is going to have my head,” John told her.

“Mmmm… they don’t like me that much,” Elizabeth said, her voice barely above a whisper.

“Well, they like me even less,” he replied.

“Don’t know why…” she said. Sheppard couldn’t figure out if she was being sarcastic or not.

“Probably something to do with my ‘problem with authority’,” he said with a laugh. It hurt his ribs.

“It’s ridiculous…”

“Nah, I get it.”

Elizabeth shook her head emphatically before answering.

“You make me feel safe.”

John didn’t know what to do with that. He tightened his hold on her and kept his mouth shut.

“McKay said it shouldn’t be much longer,” Ronon called from where he was carefully shifting rocks. If he found Sheppard and Weir’s current position strange, he didn’t let on.

“Elizabeth, we’re almost out of here and then we can get you to Beckett. I need you to hold on a little longer. Stay with me,” John said quietly, leaning down so his lips were almost brushing the top of her head.

Elizabeth made an affirmative noise and shifted a little, somehow snuggling closer to him.  

Yeah. This was definitely going to kill him.

Notes:

Quote prompt from the blog creativepromptsforwriting on tumblr.

Chapter 4: “The amount of drunk that I was or was not has no correlation to the bad decisions I made.”

Summary:

John Sheppard is having a rough morning after a drunken bet with Ronon the night before. Elizabeth Weir, along with the rest of the expedition, thinks it is hilarious.

Note: This takes place sometime after Season 3, Episode 2, when Woolsey visits Atlantis for the first time. Canon compliant, just expanded. Fluffy found family nonsense.

Notes:

(See the end of the chapter for notes.)

Chapter Text

Lieutenant Colonel John Sheppard was groaning loudly at a table in the mess hall by the time Elizabeth made it to breakfast. The rest of his team, however, were laughing loudly.

“What happened to you?” she asked, setting her tray next to him. Teyla looked down to her food in an attempt to hide her smirk. Rodney and Ronon didn’t even bother.

“I don’t want to talk about it,” John responded. He was resting his head on one arm and the other was stretched out across the table. He looked ridiculous.

“Oh, this I have to hear,” Elizabeth said, smiling wider. She took a sip of her coffee before starting in on her breakfast.

“Sheppard thought it was a good idea to challenge Ronon to ‘feats of strength’,” McKay said.

“He was very drunk,” Teyla explained with a smile.

“Excuse me. The amount of drunk that I was or was not has no correlation to the bad decisions I made,” John protested, his voice muffled from be directed toward the table.

“He’s got a point,” Ronon agreed. “He still would have done that shit sober.”

“Perhaps you are right. But I do not think it would have gone as far without the help of the mead from M48-L94,” Teyla remarked.

“How far did it go?” Elizabeth asked.

“Four of our military personnel and two Athosians” Rodney said.

Sure enough, when Weir looked around the mess, she saw a few soldiers suffering similarly—including Major Lorne.

“Anyone going to tell me what actually happened?”

“They competed in various ways to see who was the ‘strongest’. A footrace, climbing up a building, lifting heavy things in different ways…” Teyla said.

“Climbing up a building?” Elizabeth asked incredulously.

“It was a small building,” John said defensively, without raising his head.

“It went on late into the night and many bottles of mead were consumed,” Teyla continued.

“Who won?”

“Who do you think?” Ronon said with a smirk.

“I got up the building the fastest,” John said.

“But Ronon won the rest,” McKay finished, smirking himself.

“And you didn’t try your hand?” Elizabeth asked with a laugh.

“No, no, no. I know my limits. If they want to have a test of mental acuity, that would be a different story."

"I would have won that too," John said.

“No, you wouldn’t. The simple fact that you’re in the current—” McKay sputtered.

“You’re right. Zelenka would’ve.” Elizabeth didn’t have to see John’s face to know that he was smiling. She had to duck her head to hide her own. McKay made multiple sounds of outrage. She saw Zelenka grinning at the next table over.

“So now they’re all hungover and sore,” Ronon finished, sounding incredibly proud of himself.

“Colonel Sheppard?” Weir asked.

John grumbled in response. Elizabeth couldn’t keep the grin off her face. She was going to enjoy giving him hell for the rest of the day.

“Don’t we have a meeting with Mr. Woolsey in twenty minutes? And then I believe you promised to walk the new members of the Daedalus around on a tour of the main parts of the city.”

“No, I’m good,” John said. “Ronon can take them. And talk to Woolsey.” Ronon and Teyla started laughing.

“You know, I think the crew from the Daedalus were really looking forward to getting to meet the legendary Lieutenant Colonel John Sheppard,” Elizabeth said, putting a hand on his shoulder.

“He’s overrated,” he muttered, shaking off her hand and then promptly groaning. She laughed, along with the rest of the table. And a few people at the neighboring tables. Sheppard sure knew how to put on a show.

“Colonel Sheppard…” Elizabeth said, her voice coaxing.

“Fine,” John grumbled. And with an incredibly over dramatic stretch and groan, the ranking military officer of the Atlantis Expedition managed to get to his feet.

Weir had definitely seen him look better. She would have bet money that he’d puked sometime last night. But somehow, she didn’t think that would be appropriate.

As they made their way out of the mess, John walking as stiffly as possible, he was followed by applause and good-natured cheering. Evidently, tales of the escapade had traveled around.

Elizabeth waited until they got out into the hallway before turning to face him.

“You know, I think your pain may be good for morale. Maybe we should make this a regular occurrence.”

He looked at her for a moment, eyes narrowed.

“Traitor.”

“Come on, John. You’ve got a full day ahead of you.”

Notes:

Quote prompt from the blog creativepromptsforwriting on tumblr.

Chapter 5: “You said you would stay safe. Getting shot isn’t staying safe!”

Summary:

John Sheppard comes back from a mission with a new bullet wound and Elizabeth Weir takes issue with it. But don’t worry, the bullet just clipped him.

Note: Takes place in season 2, sometime before episode 17 “Coup D’etat” when Laden Radim takes over leadership of the Genii. Mostly canon compliant. I just give John a new scar. Two idiots in love.

Notes:

(See the end of the chapter for notes.)

Chapter Text

“Dr. Weir, Sheppard’s team just radioed in. They’re coming in hot and need a medical team,” Chuck reported. Weir hit the alarm and walked up to the window overlooking the glowing stargate.

“Dr. Beckett, AR-1 has radioed in with a medical emergency. Please get a medical team on standby,” she ordered, watching the response team take formation below.

AR-1 was supposed to be on a reconnaissance mission on a planet with a Genii stronghold. She really had to stop sending Sheppard’s team for reconnaissance missions. It always ended in a fight.

To be honest, Elizabeth hadn’t been a fan of the mission in the first place. And if the Genii weren’t causing problems for Atlantis at the moment, she didn’t want to poke the bear. Sheppard had promised they’d stay quiet, undiscovered, and safe. Obviously, things had not gone to plan—as usual.

McKay made it through the gate first, quickly followed by Teyla, who’s P-90 was still aimed at something on the other side of the wormhole.

“Close the gate as soon as they’re through!” McKay yelled.

A second later, Ronon and Sheppard jumped through, both men rolling to a stop on the ground. Just a hint of fire and heat made it through the wormhole before Chuck slammed the button to close the iris. The gate lit up white with a roaring sound for a solid 15 seconds before the wormhole finally closed.

Weir shook her head, irritated, as she left the control room and jogged down the stairs.

“Colonel Sheppard! What happened to a quiet, undiscovered, and safe?” she asked sharply.

That’s when she noticed that both Teyla and Ronon were gathered around Sheppard, who hadn’t gotten off the ground yet.

“Carson! Sheppard took a bullet to the abdomen about two minutes ago,” McKay said to the doctor and his team.

Elizabeth stepped closer to the group as Carson moved Ronon and Teyla out of the way. Sheppard had his hand pressed against his left side, his face white and scrunched in pain.

“It just clipped me. Rodney is being dramatic,” Sheppard said, but his voice was tight.

Elizabeth saw how much blood was leaking through his hand and wasn’t sure she believed him. Carson quickly instructed his nurses to get Sheppard onto the gurney. Sheppard clenched his teeth in pain as they moved him but remained conscious. She watched them wheel him out of the room, resisting the urge to go with them. She would just be in the way.

“What happened?” Weir asked, turning her gaze to the rest of AR-1.

“We were staying a safe distance away, just taking a look at the Genii stronghold,” Rodney explained. “They must have gotten some new technology. They knew we were there and were on us before we could even get comfortable.”

“Colonel Sheppard was hit during our retreat. Ronon was able to carry him back to the gate, but the Genii threw a grenade after us. That was the explosion you saw after the iris was closed,” Teyla finished.

Ronon had gotten back to his feet and was pulling at his now bloodstained shirt, saying “I’m going to change.”

“It can wait until after the debrief. My office, let’s go,” Weir said. She was pretty sure Ronon made a face at her, but she chose to ignore it.

 

After a full debrief and time to record some notes for her report, Elizabeth headed toward the infirmary.

By the time she walked through the doors, a nurse was wrapping a thick white bandage around Sheppard’s abdomen and Carson was making notes in his computer.

“Is he going to be alright?” she asked the doctor, walking right past Sheppard. Her ranking military officer made a face at her.

“Aye, he’ll be fine,” Carson said, sounding exasperated. Weir could relate. “He wasn’t wrong, the bullet really just clipped him. It bled a good bit, so we’re going to have him on fluids for a while until he regains his strength. But he should be right as rain before too long. Just another scar to add to the collection.”

Elizabeth finally looked back at Sheppard, who was flashing his best smile to the nurse who had just finished wrapping him up. She resisted rolling her eyes as the young woman blushed. At least John felt up to flirting. He was still pale, but the drugs seemed to be doing their job. And with him currently wearing nothing above his waist but his dog tags and the bandage, Elizabeth could see what Carson meant by his last comment.

The most prominent scar Sheppard had was in the center of his sternum, bringing Elizabeth back to watching him be tortured by the Genii. The puncture marks across his neck were still visible from when the iratus bug had almost killed him. And then there was the gunshot scar on the bicep of his left arm. She remembered that one too. Or at least remembered Rodney awkwardly escorting a bleeding Sheppard from the jumper bay to the infirmary.

“Elizabeth,” John finally said, his voice a touch wheedling. Weir raised an eyebrow.

“Colonel Sheppard.”

“Hey! We only did what I said we would. Didn’t get within 50 yards of that place.”

You said you would stay safe. Getting shot isn’t staying safe!

John held up his hands in mock surrender before wincing and letting them drop.

“It just clipped me.”

“John,” Elizabeth said, trying to instill as much authority into her voice as possible. “As the ranking military officer of this expedition, you need to stay alive and fit for duty. Taking stupid risks isn’t part of the assignment.”

“It wasn’t a stupid risk,” Sheppard protested. “It was a calculated risk. I even had McKay do the calculating.”

“You got shot!”

“It just clipped me!”

Elizabeth glared at him. He glared right back. Finally, she sighed and rubbed her temples.

“John,” she said, moving to perch on the edge of his bed. His eyes widened and flicked down to where she had sat down, just inches from his thigh. Elizabeth placed a hand on his shoulder.

“I need you to stay safe. Doing this without you is not something I want to entertain,” she said, lowering her voice. The nursing staff did not need to hear this conversation. As it was, the entire expedition would be hearing about the first part as soon as the next shift changed.

She was also pretty sure that Major Lorne was going to have a bit more spending money than normal. He was in a betting pool on how often AR-1 ran into trouble, especially on missions that were supposed to be safe. Elizabeth pretended not to know about it.

“Elizabeth, I swear. They came out of nowhere. There was nothing we could do,” he said, matching her volume. “And the doc says I’m going to be fine.”

“Next time you might not be so lucky.”

“That’s the job, Dr. Weir.”

Elizabeth paused, looking at John and trying to figure out what he meant. He looked at her back, a bit haggard, but honest. Finally, she sighed and gave his shoulder a light squeeze before letting go.

“Rest up, Colonel Sheppard. We need you back out there.”

“Yes ma’am.”

Notes:

Quote prompt from the blog creativepromptsforwriting on tumblr.

Chapter 6: Bad Dreams

Summary:

Years apart, both John Sheppard and Elizabeth Weir wake up from worst case scenario nightmares.

Note: The first part of this fic takes place during the second half of season 2. The second part takes place after the events of Season 4, Episode 10 “This Mortal Coil”. Canon compliant—Elizabeth and John are confirmed to be in love with each other, but nothing ever happens about it. First part is hurt/comfort. Second part is all hurt, no comfort.

Chapter Text

The world around her seemed to be spinning, but John Sheppard was standing in front of her, steady as ever. He was paused on the staircase, looking at her. Waiting for her to give him permission to die.

“I have to. And you know it.”

His voice seemed so much louder than it should have. Elizabeth was sure she shouldn’t be able to hear it over the explosions and shouts. He was looking at her earnestly, begging her to let him do this. He could save everyone. But she would have to give the order.

“Go.”

The gate room flashed away, and she watched as he piloted the jumper into the hive ship. She saw him close his eyes before detonating. Elizabeth felt paralyzed as John began screaming, burning, dying. There was nothing she could do. And she had told him to go. She had told him to die.

She turned away and she was back at Atlantis. John was laying prone, drained of life, against the gate. His shirt was ripped away and there was a bloody gash on his sternum. He was dying, but he was dying slowly. Painfully.

“Elizabeth…” he rasped. “Kill me. Please.”

Suddenly there was a gun in her hands. She raised it, shaking. John looked at her, begging, his eyes the only thing she recognized. Elizabeth took a step backwards, her heart slamming in her chest. The gate started dialing, those now familiar constellations gleaming. She stumbled away just in time before the wormhole exploded out.

And backed into something hard. A scaly hand wrapped her arm and spun her around. The barrel of the gun pressed into John’s chest. Half of his face was covered in rough, blue chitin. His eyes were no longer familiar. Reptilian yellow, with slits for pupils.

“Kill me,” he said, his voice low and angry. “You have to. And you know it.”

She could feel his claws digging into her arm. She fired three times. John fell to the ground, pulling her with him. It felt like they were falling forever.

And then Elizabeth woke up with a start.

She was sitting at her desk, in her office, the light streaming through clear walls. Her tablet was sitting in front of her, Colonel Sheppard’s performance reviews still on the screen. She must have fallen asleep while working.

It had all been a dream. John Sheppard was not dead. He was currently driving her up the wall by refusing to take performance reviews seriously. He wasn’t even off world.

But her heart continued to beat too fast, and she had enough adrenaline to run the entire city. Elizabeth tried to take deep breaths, tried to bring herself back to reality. She tried to focus on what she was seeing, hearing, feeling… but all she wanted to do was see him.

Finally, she gave up. Ignoring the strange looks, Elizabeth almost ran out of the control tower. She took the nearest transporter to her best guess at John’s current hiding spot. For instantaneous travel, it still felt like forever.

Finally, she walked out onto the pier closest to his room. Sure enough, her ranking military officer was sitting on a tall deck chair, his long legs propped up on the railing. He was reading the second Lord of the Rings book—Carson had lent him a copy—with a surprising amount of concentration and Elizabeth was pretty sure it was the best thing she’d seen in a while.

She stood there for a moment, just reassuring herself that he was there, before whatever sixth sense the Colonel had clued him in to the fact he was no longer alone.

“Dr. Weir,” he said, pulling his legs down and greeting her with a grin.

“John,” she answered. “Sorry to intrude…” Elizabeth trailed off. What was she going to say exactly? Sorry, I had a bad daydream about killing you and needed to make sure you were still breathing?

He waited for a moment, a look of slight concern on his face. When she didn’t finish, he gestured to the chair next to him.

“Care to join me?”

“I don’t want to interrupt your reading,” Elizabeth said, already making her way over.

“Eh. I’m at the boring part anyways. They’ve been walking to Mordor for at least a hundred pages.”

“Alright.” She pulled herself up into the chair and started to feel herself relax. Elizabeth understood why John so often deserted his office for working outside. There wasn’t much that could beat the view of Atlantis in the sunshine. And there wasn’t much that could beat her present company either.

 

His world was breaking down around him, but John remained perfectly still, his ARG aimed at the replicator Elizabeth had on his knees. The hallway was dark and growing darker around her, almost fading away, but she remained crystal clear.

“If you don’t leave right now none of us will get out of here. So, go, that’s an order!”

He yelled her name, barely hearing Ronon urging him to come. John turned, hating himself. The hallway leading to the jumper seemed to stretch out in front of him, too long to be right. Too long to make it there in time.

“John!” The shriek came from behind him. From around the corner.

“John! Save me! They’re going to kill me! John!”

And then her scream ripped through him like a bullet. He spun out of Ronon’s grip and charged back around the corner, somehow running straight into the gate room back at Atlantis.

Elizabeth stood in the middle of the room with her hand buried in Teyla’s head. He could see the bodies of McKay and Ronon, eyes wide open and unseeing.

He tried moving, tried shouting, but nothing happened. He was frozen.

Elizabeth removed her hand from Teyla’s head, and the Athosian collapsed to the floor. She was dead. Dead like the rest of them.

When Elizabeth turned to face him, he still recognized her. She still looked the same. But her eyes… her eyes weren’t right. They glinted silver every time the light hit them. Replicator silver.

“Hello, John,” she said, her voice like silk. She took a few steps towards him, hands up in a placating gesture.

“You don’t need to be afraid,” Elizabeth said soothingly. She was right in front of him now, resting her hand on his chest, above his heart. Her touch felt like fire. It was searing him down to his bones.

She put her other hand behind his neck, pulling him closer to her. He had nothing in him to fight her with. She leaned forward until her lips brushed against his ear.

“I’ll make sure you don’t feel a thing,” Elizabeth whispered. Her fingers curled into the hair at the bottom of his skull, her nails scraping almost painfully against his skin.

John was going to let her kill him. He knew that now. Everyone was gone. He had failed every single person he’d ever loved. So he leaned into her, putting his hands on her hips. If John looked into her eyes straight on, they didn’t glow silver. They were the eyes of the woman he’d fallen in love with. He could pretend it was his Elizabeth.

“Goodbye, John,” she said softly, caressing his face with her fingertips.

Elizabeth didn’t lie. When her arm morphed into a blade and plunged into his abdomen, all he felt was a growing numbness. No pain. Eventually his legs gave out. She let him drop to the floor, nothing more than an obstacle she had removed.

By the time John was able to wrench himself out of the nightmare, he was drenched in sweat and tangled up in the sheet. His breath was coming in painful gasps as he relived Elizabeth killing him, killing everyone, over and over again. The walls of his room felt like they were closing in on him. He pushed his way out of his bed and got out of the room as quickly as possible.

At first John was just walking aimlessly, trying to give the adrenaline racing through his blood somewhere to go. Eventually, he ended up on the pier.

John collapsed onto one of the deck chairs. Each breath still felt like he was wrestling it out of his lungs. He still saw Elizabeth’s eyes glinting silver every time he closed his own.

He focused on the feeling of the sea breeze across his skin and the salty taste that stuck in his throat. He matched his breathing to the rhythm of the ocean water hitting the city. Minute by minute, John could feel his body relaxing, giving up the tension from the nightmare. When it was finally all gone, he felt weak and exhausted.

More than anything, he wanted to see her again. To make her laugh and see her smile while rolling her eyes at him. To watch her expression while she was figuring something difficult out and be surprised by one of her hugs.

But Elizabeth was gone. Dead. She had been for months. And there was nothing he could do to fix it.

Sitting in the place they’d spent so much time together, listening to the waves Elizabeth used to swear she couldn’t sleep without, John felt more alone than ever before.

Chapter 7: "I Love You"

Summary:

Elizabeth Weir enjoys a quiet morning with the man she loves.

Takes place about two years after the events of Season 4, Episode 2 “Lifeline”. Except in this fic, they were able to rescue Elizabeth when they got back on the Apollo. Definitely not canon compliant. Fix-it fic. Absolute fluff.

Chapter Text

Elizabeth still woke up with the sun, even now that she didn’t really have somewhere to be. The complete opposite of the man still dead to the world in the bed next to her. Once he managed to fall asleep, she was pretty sure John could sleep until the afternoon if he didn’t set an alarm. And, when he felt safe, he could sleep through just about anything. Elizabeth didn’t need to be careful getting out of bed or tiptoe to start the coffee maker.

That was one of the things that had changed over time. When they first started to share a room, John jolted awake at the slightest sound. Even when he tried to fake sleep in the early morning so she wouldn’t feel bad, Elizabeth knew he was awake the moment she moved. Probably a combination of PTSD and being used to sleeping alone. Now, he was sprawled out across their bed, his face soft and glowing in the rising sun. Stereotypical or not, sleep was the only time John looked calm and at ease. One of the many reasons Elizabeth relished her early mornings when he was still fast asleep.

But today, John was going off world with the team and needed to be in the gate room in an hour and a half. After pouring herself a cup of coffee, Elizabeth leaned down and kissed his cheek. He made an unhappy little noise before rolling away from the sunshine streaming in. She smiled. Grumpy morning John was one her favorites.

“There’s coffee in the pot,” she said softly. He grumbled under his breath and flopped over so his face was buried in the pillow.

Elizabeth giggled to herself as she opened the door onto their balcony. John had pulled rank to get them a little apartment with a balcony when they finally decide to move in with each other. It was a few stories up, with a stunning view of the city. They’d moved about a year ago, after a new food source had been found for the Wraith and they’d found a tentative peace.

Teyla had thrown them a traditional Athosian housewarming party. Ronon had smashed the bottle of red wine Rodney brought against one of the walls. She could still see the stain when the light was right. Moving in with John was one of the best decisions she’d ever made—second only to joining the Atlantis expedition to begin with.

She’d finally thrown caution to the wind two years ago, right after she had almost died on the replicator home world. There had been something on his face when she had woken up in the hospital; haggard, exhausted, and utterly relieved. As much as she had wanted to hide away—she hadn’t been able to get Oberoth’s voice out of her head yet—having him by her side had made things easier. When she was released from the infirmary a week later, Elizabeth went straight to find John. He was sitting on one of the more secluded piers, looking like he’d been to hell and back.

She had been removed from command—understandable—but not allowed to return to earth. She had been compromised, so she couldn’t be in charge anymore. But she couldn’t go home either. That would be a security risk. General O’Neill assured her they would find her a role. The only thing that really mattered to her in that moment was that John Sheppard no longer reported to her. They’d been together ever since.

Elizabeth loved seeing the last few minutes of the sunrise while sipping coffee out on their balcony. Sometimes she would spend the first hour of her day out here, especially when John slept in. This morning it took about fifteen minutes for him to finally get out of bed, wrap himself in the ridiculously soft robe she had bought him for his birthday, and join her on the balcony with his own cup of coffee.

He came to stand next to her, casually wrapping his arm around her waist. She rested her head on his shoulder. It had taken them a while to get to this relaxed with physical affection. Elizabeth had always been a touchy-feely person. John was not. The first time she’d hugged him, he’d frozen completely. The next few times weren’t much better. But they’d worked on it, together.

They stayed like that for a few minutes, looking out across the ocean, before John needed to move again. He took his arm off her waist and held his coffee cup with both hands, but still stood close enough that their shoulders were touching.

“Looks like it’s going to be a beautiful day,” Elizabeth said.

John nodded, his mind already through the gate and thinking about the mission to come. While they were technically at peace with most of their former enemies, something could always go wrong. AR-1 knew that better than most.

“Be safe out there,” she said, reaching over to gently squeeze his arm. He gave her a crooked grin before planting a kiss on her lips.

“I’ll do my best.”

He never promised to be safe. Not when they both knew he’d jump in front of a bullet to save someone, anyone, without thinking twice. Elizabeth supposed that should worry her. But that innate desire to protect was one of the things that drew her to John in the first place. It seemed silly to dislike it now. Although that didn’t mean she’d ever stop reminding him to come home to her.

John yawned loudly and stretched his long limbs out as far as they would go. So dramatic.

“We shouldn’t be gone too long. I’ll see you this afternoon,” he said, draining the last of his coffee and turning to go.

“Good luck,” Elizabeth said. “I love you.

John smiled back at her.

“Love you, too.”

Chapter 8: Bureaucratic Military Bullshit

Summary:

After a difficult meeting with Stargate Command, Elizabeth Weir is reminded why she doesn’t like working for the military. With one exception.

Note: Takes place between the events of Season 2, Episode 1 “Siege, Part 3” and Season 2, Episode 2 “Intruder”. Loosely based on the flashbacks seen in “Intruder”. Canon compliant, technically. Two idiots in love.

Chapter Text

Dr. Elizabeth Weir left her latest meeting at Stargate Command with a pounding headache and in a foul mood. There had been no time to celebrate, or even take a breath, since they tricked the Wraith into thinking Atlantis had been destroyed. As soon as they reopened the gate to Earth and explained the situation, General Landry and the I.O.A. had ordered them back. Or really, they had ordered her back.

The request had been to fully debrief the past year and discuss additions to the expedition. She had insisted on bringing her senior staff, since it was ultimately their decision on who to bring on. The only slight pushback she had gotten from the brass was on bringing Major Sheppard. They had suggested he would be needed to keep an eye on things. Now she knew why.

The I.O.A. had the audacity to act like Sheppard wasn’t fit for the job, especially after a year of him often being the only reason they survived. The negotiator in her understood the position they were in, considering everything that had happened with Colonel Sumner. John was headstrong, always thought he knew best, and had a remarkable knack for getting people to see things his way. Sometimes to their own detriment. But the part of her that had been fighting alongside him for months just to stay alive; the part of her that kept playing the moment he had gone to die over and over in her head… well, that part was pissed.

There was a reason Elizabeth hadn’t worked with the military before the President had asked her to be the head of the SGC. The higher ranked officers always reminded her of angry bulldogs, snuffling around in indignation . They rarely had any interest in what a civilian had to say, especially a diplomat. And the younger soldiers… they usually made her think of some cross between a golden retriever and a german shepherd. Equally energetic, eager to please, and constantly ready to escalate things to a fight. And equally uninterested in what she had to say.

The soldiers tangentially under her command on Atlantis had always treated her with respect, but everyone knew that they would follow Major Sheppard’s orders before her own. Most of the time it didn’t bother her. But then again, most of the time Sheppard and her were in agreement. There hadn’t been a lot of moments that tested that tension or pushed the unclear chain of command. Working with the Major and being cut off from the earth for almost a year had almost made her forget why she didn’t like the military to begin with. Almost.

Trying to keep the scowl off her face, Elizabeth made her way to the mess hall. The last meeting had gone thirty minutes past when it was supposed to let out for lunch. She was starving. At least the food at SGC was better than what they could get their hands on in Atlantis.

When she walked through the doors, the first thing she saw was John Sheppard, focused on what seemed to be a riveting conversation. Elizabeth took a moment to watch him, talking animatedly with a man she didn’t recognize and half sitting on a table. John always reminded her a little bit of a cat. Always perching on surfaces he shouldn’t—like her desk or one of the railings outside the command tower. He also seemed to carry the same calm, coiled energy. John was all lazy, long limbs until it was time for him to spring into action. Then he was almost unstoppable. Plus, Elizabeth was pretty sure he would agree with a house cat’s penchant of knocking things off counters. Just on principle alone. He had a tendency to push peoples’ buttons just to see how annoyed they’d get.

Elizabeth smiled slightly at the thought before shaking her head and heading toward the food line. As she walked along the side of the tables, she noticed all the people who were watching Sheppard. Some people were just staring outright, others watching him out of the corner of their eyes. Mixed expressions. She saw a few glares of anger and disgust—people who had served with Colonel Sumner and clearly didn’t understand how he died, if she had to guess. Some people were just looking on in interest. And quite a few were looking at him with unabashed admiration or attraction. Elizabeth wondered if he even noticed. Probably not. He most likely just noticed the glares.

She had just put some blue jello on her tray when she heard her name being called out. Major Sheppard motioned her over to an empty seat. He gave her one of his customary grins when she set her tray down at his table.

“Dr. Weir, this is Major Evan Lorne. He’ll be joining us on Atlantis. Major Lorne, Dr. Elizabeth Weir,” John said.

“It’s nice to meet you, ma’am,” Major Lorne said, holding out his hand.

Elizabeth smiled and shook the young man’s hand, but all she could focus on was just how young he really was. Definitely more golden retriever than german shepherd. Though he was currently wearing a uniform with an SG-11 patch, so he must not be as young as he looked. And it seemed like he at least had experience with off-world travel. Some of the people General Landry was trying to send to Atlantis were lacking that particular skill set.

It took her a moment to realize John was telling Major Lorne about her. How she had waited thousands of years to save the expedition. It felt like an odd compliment. It wasn’t really even her. But it seemed to be having the desired effect on Major Lorne. He was looking at her with wide eyes and a new glimmer of respect that came from more than her position.

“Major Sheppard!” Colonel Caldwell barked from the doors of the mess.

John glanced over at the superior officer, just how unimpressed he was written all over his face. Elizabeth wondered when things had changed. The last she had seen them together, John was treating him with the respect due someone who had just saved his life. Now the Major was looking at the Colonel like he wasn’t much more than a particularly annoying gnat.

“You’re due for a meeting with General Landry,” the older man said authoritatively. Elizabeth cringed internally. That was not going to go over well.

“Not for another five minutes, Colonel,” John said, a shit eating grin on his face. “And it only takes me three to walk down there.”

Elizabeth glanced down at her plate to hide her grin. Out of the corner of her eye, she noticed a few others doing the same. Caldwell looked like he would have gladly hauled Sheppard to a court martial for insubordination. But instead, he just stood at the door, glowering and waiting.

John shrugged and grabbed his tray.

“Lorne,” he said with a goodbye nod. “Doctor.”

“Behave, John,” Elizabeth told him, keeping her voice low. He gasped in mock offense before flashing her a smirk and heading toward door. Major Lorne chuckled softly. Evidently Sheppard had already won him over. He had that way with people, when he wanted to use it. Elizabeth had come to rely on his easy ability to get people to follow him, and more importantly, to trust him.

Watching the Sheppard walk away, Elizabeth sincerely hoped the SGC would listen to her. She didn’t want to face Atlantis without John by her side.

Chapter 9: Meaningful Glances

Summary:

Stargate Command and the I.O.A. throw a party for the returning members of the Atlantis Expedition. Unexpected feelings are stirred up.

Note: Takes place between the events of Season 2, Episode 1 “Siege, Part 3” and Season 2, Episode 2 “Intruder”. Canon compliant, technically. If you really like Dr. Simon Wallace, this fic is not for you. This fic can be connected to the next chapter—but both can stand alone.

Chapter Text

Elizabeth Weir walked through the hallway leading to the largest empty hanger in the Cheyenne Mountain base with her fiancé. The I.O.A. and the US Government were throwing a ball to celebrate the return of the Atlantis Expedition members. Stargate Command—mostly General Landry—was strongly against the whole idea, but the higher ups thought it would be a good idea for courting continued foreign support.
Elizabeth, on the other hand, loved the idea. After almost a year of constantly fighting for her life, it would be nice to have a night of fun and good food. Even if she had to play politics for the duration. She had even decided to buy herself a new dress. A dark green, halter neck floor length gown with a low back—just a bit more daring than she would have picked a year ago. And it showed off the results of all that training with Teyla. Simon hadn’t said anything when she came out of their room, but he had raised an eyebrow in appreciation.

When they walked up near the door, Elizabeth could see her senior staff off to one side, along with the members of SG-1 and General Landry. This is where she and Simon would split for a moment. He was used to these events and used to walking into them without her. Most of the time she was part of the delegation that made a grand entrance and tonight was no different. She gave him a quick kiss on the cheek before he walked through the doors to find their seats. Then Elizabeth headed toward her team.

“Why are we doing this again?” She heard McKay complain as she got closer. Elizabeth smiled to herself. It appeared she was the only person looking forward to tonight. Except, on further examination, perhaps Carson was as well. The doctor looked particularly well dressed in a three-piece tweed suit.

“Do you have something against a party, Dr. McKay?” Elizabeth asked, walking up to join the two doctors.

“No, I’m just not so sure why throwing an expensive ball for an expedition no one can even know about is the best use of our time or resources,” he said stubbornly.

“McKay’s just mad the I.O.A. forced him out of his lab,” John said, walking over to join their group. He paused a moment when he caught sight of her, and the look on his face was not one she could easily decipher. Which in and of itself was odd. Elizabeth had gotten good at reading him over the last few months.

Then she took in the rest of him and felt herself hesitating as well. This was the first time she had seen Major John Sheppard in anything but his black t-shirt and Atlantis uniform jacket. He was in his Airforce dress blues, every bit of him button upped, shined, and ironed to perfection. It gave him an aura of respectability and command that she hadn’t noticed before. And it was only slightly ruined by his perpetually messy hair and the tie still hanging undone around his neck.

“Major,” she said, by way of greeting.

“Doctor,” he responded with a grin. That crooked smirk brought him a little closer to the man she was used to working with.

Elizabeth smiled back and him and took a step closer to tie his tie for him. John made a disgruntled noise but let her finish. She smoothed out his lapels before patting him on the chest gently. There was still a part of her that marveled at the fact he was still alive. That they both were. She didn’t think she would ever forget how it felt to watch his jumper explode on the sensor. Or how it felt to hear his voice over the radio. And if the look in his eyes right now was anything to go on, he felt the same.

Elizabeth had no idea how long they had both been standing there when General O’Neill walked up and cleared his throat. John immediately took a step back.

“General,” she said with a smile. “It’s good to see you again.”

“Doctor Weir,” he responded, glancing between her and Major Sheppard. When he turned back to her, she couldn’t quite identify the look on the general’s face. Understanding, maybe?

“We’ve got a few more minutes before it’s time to make our grand entry,” General Landry said, walking up. The rest of SG-1 followed. There was a quick moment of introductions. Elizabeth already knew T’ealc, Colonel Carter, and Dr. Jackson, of course, but Colonel Cameron Mitchell was a new face. McKay was predictably flustered by Carter and Carson was predictably charming to the whole lot of them.

Eventually a young woman with a clipboard came forward to get them ready to walk in. She carefully positioned everyone in the correct order and pairing. Elizabeth and Major Sheppard would be walking in together.

“All this for a thirty second walk?” John mumbled under his breath.

“You’ve never done anything like this before?” she asked.

John gave her a look.

“Let’s just say I wasn’t high on the Airforce’s list of people to invite to fancy parties,” he responded, tugging at his tie until it was looser and incredibly crooked.

“I can’t imagine why,” Elizabeth said lightly. Then she reached up and fixed his tie for the second time. He rolled his eyes and made a face. For all his making fun of Rodney not wanting to be here, it was abundantly clear that he wanted to be anywhere else.

But when it came time to walk into the party, Major John Sheppard straightened up and offered her his arm like a proper Airman. Almost worthy of the promotion to Lieutenant Colonel he’d be getting tonight. Not that he had any idea. She had only gotten the confirmation this morning. The SGC and I.O.A. were letting him stay. They had listened to her. Elizabeth smiled up at her Ranking Military Officer as they walked through the double doors and into the bright lights of the party.

When Dr. Simon Wallace watched his fiancé walk into the room, he was struck with a feeling he was unfamiliar with. He was used to watching from the sidelines as Elizabeth made her grand entrances. It had never bothered him before. Simon usually enjoyed everyone looking at the beautiful, successful woman that belonged to him. Especially when she made her way to their table and sat down next to him. The lifesaving doctor and the savvy diplomat, both known the world over. They made quite the couple.

Tonight was different. Something ugly curdled in his gut as she walked in, beaming, on Major Sheppard’s arm. Elizabeth had talked about the Major, of course. She had shared the stories she could without violating her nondisclosure agreement. Simon had noticed the tone she used—almost reverent at times. It had rankled at first, his mind warring between being grateful Sheppard had kept Elizabeth alive and jealousy that someone else had that important a place in her life. Before she had gone off to save another galaxy, he alone was that important to her. Eventually, as Elizabeth had moved on to the talking about the rest of her team, Simon had been able to write it off as a close working relationship. She spoke in glowing terms about all her senior staff. The only thing that made Major Sheppard different than the rest was the amount of time they spent working together. That was all.

Now, he felt completely different. Something in the way Sheppard looked at her rang every warning bell in his head. The man was looking at his fiancé like she was the sun his whole damn galaxy revolved around. And Elizabeth… Simon had never seen her look so comfortable and at ease. This was someone she trusted implicitly, without reservation. Elizabeth had never looked at him like that.

Anger built up inside him, clawing up his throat and causing enough tension he had to hide his fists underneath the round table. How dare she. How dare she move on and choose someone like that over him. He was a doctor. He saved people, constantly pioneering new treatments and new surgeries. Simon’s entire life revolved around doing no harm. And Elizabeth had left him for a killer.

John Sheppard had more blood dripping from his hands than most inmates on death row. Even before the mysterious death of his Atlantis commander, Sheppard was so reviled by the Airforce he’d practically been banished to Antarctica. All the times he’d saved Elizabeth were only possible because of his capacity for violence—his tendency to shoot first and ask questions later. This was the man his fiancé was choosing over him. He’d never understand it.

Simon’s thoughts drifted to the beautiful, brilliant scientist he had begun seeing after the expedition was presumed lost. When Elizabeth miraculously returned, he had explained to her that they needed to work things out. He needed time to figure out what moving forward was going to look like. She had understood. Now he knew his decision. He would not be spending the next year of his life in another galaxy watching Elizabeth love another man. Especially that man.

Decision made, he found it remarkably easy to smile at his fiancé as she joined him at their table. It didn’t bother Simon a bit that Major Sheppard was sitting across from them, still gazing at Elizabeth, or how often her eyes found his and lingered. What went on between the two of them no longer mattered to him. It was over. She just didn’t know it yet.

 

John felt like his tie was going to strangle him if the fitted jacket of his dress uniform didn’t smother him first. He’d mostly avoided events like this in his career—made a point of it, actually. He’d never been good at faking decorum he’d never possessed.

When they’d been told about the party, he had been halfway through making up foolproof excuse to avoid the whole thing before they’d even left Landry’s office. Then Elizabeth had turned to him on their way out with a smile so big she was practically glowing. Before they’d even made it back to their on-base quarters, she had talked about everything from the guests to the caterer to needing a new dress. It wasn’t that her excitement was infectious, John still hated the entire idea. There was something in the way she was excited to share this with him that gave him pause. So now he was sitting uncomfortably in the largest room in Cheyenne Mountain, a space so utilitarian that even the shining decorations couldn’t hide it.

Someone from the I.O.A. was making polite small talk to his left, but John was only hearing every other word. He was going to kill whoever made up this seating chart. Straight up murder them. Elizabeth was sitting directly across from him, in a dress that made him want to lose his mind. Stunning didn’t even begin to cover it. Despite doing his best to stop staring, he kept catching her eyes when she glanced up. Her responding smile made his lungs forget how to breathe every time.

John had been wrestling with it since the failed Wraith invasion. It wasn’t like the feelings were new. Elizabeth had gotten his loyalty, his admiration, the moment she’d looked at him and saw something of worth. He could count on one hand the amount of people who had done that. But it wasn’t until he was flying the jumper into the Wraith ship that he actually realized how deep those feelings were. He had stopped to ask her. Usually, he wouldn’t have thought twice about running headlong into danger, damn orders and chain of command alike. But he had stopped and she had let him go. When she had thrown her arms around him in the gate room… Elizabeth was the first person in years to embrace him that way. Like nothing else mattered in that moment.

But he didn’t have the right to feel any of that. Elizabeth was engaged to a doctor. The very opposite of everything John was. Even ignoring the obvious chain of command issues—he’d never been much for rules anyways—he could never compete with that. He would never deserve her. There was too much wrong with him. There were too many pieces of him that were gone, damaged beyond repair. John wanted more for her.

Later that evening, Elizabeth pinned a new insignia on his chest, officially giving him the rank of Lieutenant Colonel. When she looked up at him, her expression was a mix between satisfaction and pride. Then she slid her hands down his shoulders, as if straightening out imaginary wrinkles, and her fingertips felt like fire across his skin even through his uniform.

“Congratulations, Lieutenant Colonel John Sheppard,” she said softly, as if it was for his ears only.

The entire world could have exploded in that moment and John was pretty sure he wouldn’t have noticed.

Too soon, she gave him a smile and stepped aside. John barely remembered saluting Generals O’Neill and Landry or going back to sit down. He barely remembered the rest of the night. All he knew is that by the time the night was over, he was lost. He was completely and inescapably in love with her. There was no going back. But this was enough. He never would be worthy of her, and she would never love him, so what they had now was enough.

Chapter 10: Military Man

Summary:

Elizabeth Weir deals with the aftermath of a breakup and a difficult accusation.

Takes place between the events of Season 2, Episode 1 “Siege, Part 3” and Season 2, Episode 2 “Intruder”. Loosely based on the flashbacks seen in “Intruder”. Canon compliant, technically. If you really like Dr. Simon Wallace, this fic is not for you. This fic can be connected to the chapter before—but both can stand alone.

Chapter Text

It had just been a few days since Simon had ended things. He had left immediately that night, probably went back to the woman he had found while Elizabeth was presumed lost. One phone call later and they had worked out a plan to end their relationship. Simon would keep the house—it wasn’t like Elizabeth needed it anyways—and would pay her back the initial down payment. They decided he would stay away until after she went back off world. That would give her plenty of time to pack up her half of their life together.

She was boxing up the last of her things when she heard a key turn in the door. The sound made her pause since there was no way her mother could have already been back from going to drop off the latest load. The only other person with a key was the one person she didn’t want to see today.

Sure enough, when Elizabeth went into the foyer, Simon stood awkwardly at the door.

“I thought you were going to wait until after I left,” she said, resisting the urge to cross her arms. “You said you owed me that much.”

“Elizabeth, I…” he said, trailing off.

“I’m packing the last of my boxes now. The house will be all yours by the afternoon, if it’s really that urgent.”

Elizabeth walked back into the living room, intent on going back to packing.

“I came to drop off the check… and I wanted to explain,” Simon said, following her.

She took a deep breath. There was no use in getting into an argument, no matter how much she was hurting. But that didn’t mean she had to look at him.

“Put the check on the counter. And you don’t have to explain, Simon. I was gone for almost a year. I told you to move on. I understand,” Elizabeth said, going back to folding towels. She saw him set the check down out of the corner of her eye.

“You were so angry before,” he said. “I just wanted to talk to you again. Before you left.”

Elizabeth was about two seconds away from losing it. She’d given him permission and she’d absolved him of any guilt. What else did he want from her?

“I was angry, yes,” Elizabeth said carefully. “But not at you. It’s a difficult situation.”

Simon walked around so she was facing him.

“You seemed pretty angry at me.”

Why was he pushing this? What on earth was he trying to get at? Elizabeth sat down the towel she was folding and looked up at him.

“Fine. I was angry at you. But not for moving on. I was angry because you didn’t tell me. You should have told me as soon as I got home. Instead, you let me hope for days that you were coming with me. You pretended with me, when you should have respected me enough to be honest with me. That is what I am angry about.”

“I didn’t know how to tell you,” he said, imploringly. Elizabeth knew the expression he was putting on. It was the face he used every time they had gotten in fights in the past. Every time he had treated her like what she did wasn’t as important as his work. But Elizabeth wasn’t the woman he had known. She hadn’t been for a long time.

“You should have figured something out. You’re a smart man, Simon,” she replied, letting some of the acid come into her voice.

“Don’t put this all on me!” he exploded. Elizabeth took a step back.

“I’m not!” she yelled back. “I’m not pretending this was a simple situation. Most couples don’t have to contend with another galaxy’s worth of long distance. But you owed me the truth.”

“I’m not the only one who strayed,” Simon said coldly.

That one took Elizabeth by surprise.

“Strayed...? What are you talking about?” she asked, genuinely at a loss.

“I saw how you look at him.”

“Look at who, Simon?”

“Your Lieutenant Colonel Sheppard.”

Elizabeth blinked. This was not how she had expected this conversation to go.

“There is nothing going on between me and Colonel Sheppard.”

“Oh, don’t give me that. I saw the way he looks at you, too. Like you’re the ocean and he’s just begging to drown.” Simon had a snarl on his face now.

“I’m not going to pretend John and I haven’t been through a lot together, but we are friends. There has never been anything more.”

Simon shook his head.

“You know, for a diplomat, you are a terrible liar. Always have been.”

“I am not the one who lied,” Elizabeth spat. Simon had crossed a line. In fact, he had crossed several.

“Good luck with the rest of your life, Elizabeth. And with your military man,” he said. “Though how you can be with a killer like him, I’ll never understand.”

And that was it.

“Get out,” Elizabeth said, her tone low and even.

“This is my house,” Simon answered.

“This was our house,” she replied. “You can come back at 5:00. I’ll be gone by then.”

Simon took a step closer, opened his mouth like he was about to say something.

“Get. Out,” she repeated.

He backed up, eyes wide. It was like he was seeing her again for the first time. Elizabeth raised an eyebrow at him, daring him to say another word. Instead, he turned and left, slamming the door behind him. She went back to folding the towels.

 

A week later, Elizabeth was walking up to the Daedalus’ loading pad in the SGC. All crew, passengers, and cargo were getting beamed up to the ship in groups. The newly promoted Lieutenant Colonel John Sheppard was standing at the edge of the pad, his hands planted on his hips as he watched the progress. He was back in his Atlantis uniform, just like she was, even though they didn’t need to be. They were still solidly in friendly territory, but she could see his sidearm strapped to his thigh. John never liked to be unarmed.

Simon’s words came back to her. Good luck with your military man. As if that summed up all he could possibly be. As if killer was all that he would ever be. Maybe the woman she’d been before Atlantis would have balked at John’s body count. Maybe she should still be bothered by it. Elizabeth would never pretend he didn’t have blood on his hands. He wouldn’t either. But he was the bravest man she’d ever met. He consistently put himself in danger without hesitation if it meant saving lives. And he had saved her life more times than she could count. So, Black Knight or not, Elizabeth was glad to have him.

Sheppard turned to her as she walked up and flashed her a crooked grin.

“Doctor,” he said, turning his attention back to the train of supplies and people.

“Lieutenant Colonel,” she replied, cutting her eyes over to catch John’s satisfied smirk. “How is the loading process going?”

“Slow,” he said. “But we’re about halfway through with the supplies. Atlantis personnel will be loaded after that.”

“Where’s Dr. McKay?” she asked, looking around the room.

“He went up with the first load. Evidently the Daedalus’ science team couldn’t be trusted with the samples he’s bringing."

Elizabeth smiled to herself. Tempered a bit by experience or not, he was still Rodney McKay.

“And Dr. Beckett?”

“He wanted to get started on some team bonding with his new doctors. They went up about fifteen minutes ago.”

She nodded. Even with the instantaneous teleportation loading, it took a while to get a ship like the Daedalus fully stocked. Elizabeth shifted her backpack to a more comfortable position. John glanced over.

“I’m sure you could catch a ride on the next beam up,” he said.

Elizabeth saw the pile of his things sitting by his feet. She dropped her bags down next to them.

“I’ll wait,” she said. “It will be good for the new members of the expedition to see the both of us.”

John shrugged, but Elizabeth had a feeling he was happy she chose to stay.

“When is Dr. Wallace arriving?” he asked after a moment.

Elizabeth looked straight ahead, focusing on the latest pile of crates. She was pretty sure everything would come tumbling out if she looked at him.

“He isn’t joining us.”

“You okay?”

“I will be. Atlantis just wasn’t the right place for him.”

Out of the corner of her eye, she saw him shrug.
“His loss then.”

Elizabeth smiled to herself. Leave it to John to not make a big deal out of her calling off her engagement. She imagined she’d have more explaining to do when she saw Teyla again.

“Did you visit anyone?” she asked carefully. She remembered when they were filming their messages home, John had only filmed something for Colonel Sumner’s family.

“Lt. Ford’s family. I thought they deserved to hear it from someone who knew him.”

Elizabeth smiled again. Unfeeling military man indeed.

Chapter 11: Sex and Star Trek

Summary:

John and Elizabeth compare romantic pasts.

Note: Takes place a few years after the events of Season 4, Episode 2 “Lifeline”. Except in this fic, they were able to rescue Elizabeth when they got back on the Apollo. Definitely not canon compliant. Absolute goofy fluff. Completely self-indulgent. Not smut.

Chapter Text

“What about the princess on that world that almost made you king?”

“Elizabeth!” John said incredulously.

She grinned up at him from where she was laying, draped across his stomach with her legs tucked comfortably under the sheets.

“What? I’m just curious,” she said. “And you did say that ‘you got the girl’.”

“No, I said I turned her down,” he corrected her, but he was grinning back at her. And trying very hard not to get distracted by her fingertips tracing a particularly sensitive scar along his rib cage.

“So…?”

“So, no. I did not sleep with the princess,” he said. “A woman wanting to sleep with me just so she can survive isn’t the biggest turn on.”

Elizabeth looked incredibly amused—and a little smug.

“She did tackle me naked though.”

She raised an eyebrow at him. John just grinned back at her.

“And the ascended priestess?”

“Are we really doing this?” John asked.

“Why not? Embarrassed?” Elizabeth teased, folding her arms across his chest and laying her head down on them. Her hair was tousled and messy, errant curls spilling into her face. He had never seen someone so stunning. So John just shrugged, indicating his capitulation. He was pretty sure she could’ve convinced him to do just about anything in that moment.

“I did not technically sleep with the ascended priestess,” John said confidently.

“You didn’t… technically sleep with her?” Elizabeth asked suspiciously. “That’s usually a yes or no question.” Her eyes were still shining with amusement.

“We did some sort of Vulcan mind meld,” John tried to explain. Elizabeth laughed out loud.

“I’m being honest!” John insisted. “There was nothing… physical about it.”

“Ok…. I suppose that doesn’t count then.”

“Thank you for being so magnanimous,” John said.

They rested there in silence for a moment, Elizabeth bringing up her hand to gently trace the wraith scar on his sternum. Before her, John would have confidently said he wasn’t someone who liked being touched. Sure, there were certain activities that he could easily make an exception for, but, on the whole, he liked his space. With Elizabeth though, John honestly couldn’t get enough.

“What about that particularly stunning woman in the Ancient time dilation field?”

“Six months, Elizabeth. Six. Months,” he answered.

“So, is that a yes…?” she prodded, splaying her palm across his chest.

“Yes,” John admitted. “Why aren’t we talking about any of your past relationships?”

“Because I’m not the Captain Kirk of this expedition,” Elizabeth said with a wide smile. John rolled his eyes.

“You’ve been talking to McKay too much.”

Elizabeth shrugged.

“I didn’t have the same opportunities to channel my inner James Kirk,” she pointed out.

“I’m sure Lucius Lavin would have happily helped you out with that,” John said, his smile turning a bit wicked.

Elizabeth smacked him lightly across his chest.

“Not funny,” she protested. He just laughed.

“And I was engaged my entire first year in Atlantis,” Elizabeth said.

John’s expression turned serious, his eyes searching her face.

“You never talked about what happened there,” he asked carefully.

Elizabeth sighed, pulling her hand back under her head. John just waited. If she wanted to answer him, she would. If not, she’d change the subject.

“By the time we got back to earth, he had found someone else,” she said simply. “I don’t think he would have done well on Atlantis. That’s not the kind of life he wanted. And… at that point… I wasn’t the same woman he’d proposed to. I think on some level, I really wanted to be. I think he wanted me to be. But… things change.”

John reached his hand forward and gently squeezed her arm. As much as he hated to see her hurt, he was glad that relationship hadn’t worked out. He could never have competed with the doctor.

Elizabeth huffed a little laugh and rolled off him. She moved backwards until she was laying on the pillow next to him, looking up at the ceiling. John rolled over so he was facing her, propping his head up on his arm.

She took a deep breath and turned to look at him. John was surprised by the expression on her face. He had expected her to look sad. Or at least wistful. Instead, she was looking at him like he was the best thing she’d ever seen.

“I think it worked out for the best though,” Elizabeth said softly. “I was happy with Simon, I know that. But this… this is something I couldn’t have even dreamed of.” She moved closer to him, cuddling against his chest. John wrapped his arm around her, pulling her in. He could stay that way forever.

Elizabeth was silent for a while, her breathing slow and deep. John closed his eyes, the long day finally catching up with him.

“Now that I think about it… Simon did give a different reason for us not working out,” she mused. John hummed for her to go on but didn’t open his eyes. Between the warmth of her body and the pressure of the blankets, he was just a few minutes away from passing out.

“He insisted that we were in love with each other.”

John’s eyes snapped open.

“I guess he saw something neither one of us were aware of yet,” Elizabeth finished. He could almost hear the smile on her face.

John pressed a kiss to the top of her head. She might have not been aware of it yet, but John had known. He had known how much he loved her when he had paused on the steps up to the jumper bay, asking for her permission to die. And he had definitely known how much he loved her as she’d thrown her arms around him when he made it home. He just had never dreamed Elizabeth would ever love him back.
But now that he thought back to those first few years, while he held her close and with the benefit of hindsight, John could see there were signs. Moments that didn’t quite add up unless you knew how it was going to all end. He smiled, thankful beyond words for this love he had stumbled into.

Soon they were both asleep, safe in each other’s arms.

Chapter 12: Debrief

Summary:

After hours of reliving one of the worst days of his life, John Sheppard goes to Elizabeth Weir for a mission debrief.

Note: Takes place after the events of Season 3, Episode 9 “Phantoms”. It is technically canon compliant, because it doesn’t directly conflict with canon. But John and Elizabeth may be closer to each other than canon, depending on how you interpret it. I just wanted John to get a hug, damn it! Ultimate emotional hurt/comfort.

Chapter Text

It had been a long, difficult couple of days. AR-1 had been out of contact for hours after going after a team of marines that were overdue. When Elizabeth had finally heard back from John, she’d learned about their day from hell. They had been hallucinating their worst nightmares for hours. All of the men they’d gone to save were dead. One of the marines they’d taken also didn’t make it. Teyla, Ronon, and Rodney had all been shot. Carson sounded like he was ready to collapse. John said he was fine, just a little creeped out. But Elizabeth had heard something in his voice that made her think he was hanging on by a thread. She’d bought the act though, keeping her tone positive and trusting.

When they reported back in a few hours later, John still sounded off. She just thanked him for checking in and reminded him there was just a handful of hours left before the Daedalus would be there to pick them up. Elizabeth could give them time to work through it on their own and then debrief when they get back.

Once the Daedalus picked them up, it was just more of the waiting game. It was good to know that the injured were getting full medical attention and they were on their way back home, but Elizabeth still found it impossible to sleep. The hollow sound in John’s voice kept echoing through her head. So, she’d given up and gone back to her office to work on reports. This was going to be one hell of a report to write, and she hadn’t even heard the full story.

When John walked into her office an hour later, Elizabeth had her bare feet pulled up into the chair and was resting her chin on her knees. He knocked on the door jamb.

“John,” she said, unfolding herself and walking over to meet him.

“I figured you would want a debrief,” he said. The hollow quality was still in his voice and he wasn’t meeting her eyes.

She put her hand on his shoulder. He didn’t really react.

“This can wait until after you get some rest,” she responded, moving her head a bit to try to catch his gaze.

“I got some rest on the ship,” John said, his tone strictly military. “I’d rather get it done.”

Elizabeth took a step back.

“Alright. Why don’t you take a seat on the couch,” she said, gesturing to the small cream sofa across the room. She could count the number of times she’d used it on one hand. If he thought it was strange, he didn’t comment. Just went and sat down. Elizabeth rolled one of the chairs over to sit in front of him.

Quickly and methodically, John took her through the mission. His report stayed dull and technical. Nothing like the normal debriefs they’d had. Even on bad days, John still was animated, ranting through the report. This wasn’t anything she had seen from him before.

He didn’t go into detail on what he had seen. Just that it had led him to believe Ronon and McKay were enemies. After he finished, he sat in silence, staring at the space to the right of her head. Elizabeth wasn’t sure what he was waiting for. Was he expecting her to be angry? From everything she’d heard, it was a miracle AR-1 made it out at all. It was a testament to strength of the team John put together that they were all alive, wounded or not.

“You brought them home,” she said softly, shifting so she could look into his eyes. His gaze was glassy and unfocused. Like he was staring off at something an entire galaxy away.

“I didn’t bring them home. Rodney and Teyla did,” he responded, finally meeting her eyes.

“And who got Teyla to the cave? Who put that team together in the first place?” Elizabeth asked, reaching up to touch his shoulder again.

“I was next to useless, Elizabeth,” John said, his voice catching on her name.

“You carried Teyla miles to get her to safety.”

“And then I shot McKay in the chest. I could’ve shot him in the head.”

“Rodney is going to be fine.”

“And Sgt. Barris is dead.”

Elizabeth sighed. She moved her hand from his shoulder to his knee and squeezed lightly.

“Talk to me, John. What did you see?”

He looked away again. She let the silence stretch out between them.

“How much did you read about my court martial?” he asked quietly.

“Not much. I wasn’t interested in what you had done in past. All I cared about what you could do to help the expedition. And I have never regretted bringing you with us.”
“I went against orders to save my captain. He had crashed his helicopter over enemy lines. The vehicle I took out was shot in the engine block. It was useless. We had to hide in that helicopter for almost 18 hours before I could get the radio working again. By the time they could fly us out, Holland had been dead for over two hours. It didn’t matter what I risked to save him.”

John was staring off into space again, he hands sitting slackly in his lap.

“And that’s where you were?” Elizabeth prompted. This was the most he had ever talked about his past in the two and a half years she had known him.

He nodded.

“I can’t imagine what that must have been like.”

John just shrugged.

“Ronon was thrown back into his runner days. A terrible half a day is nothing compared to that.”

“Don’t do that. Don’t dismiss what you went through on that planet.”

“What, getting my entire team shot to hell?”

Elizabeth realized then that there would be no talking him down tonight. He was drowning. So, she stood up and wrapped him in a hug. Instead of freezing like he had almost every time before, John seemed to melt into her. He pressed his head against her stomach and wrapped his arms around her hips.

She wasn’t sure how long she stood there holding on to him. John didn’t break down. He didn’t cry. He just let himself be held. This was the longest he had ever let her touch him and it felt like someone was squeezing her heart in her chest. Slowly, she felt the tension drain out of him.

“Hey,” Elizabeth said eventually, moving her hands to bury in his hair. She gently scraped her nails against his scalp and felt him shudder slightly.

“You need to get some sleep,” she continued. When she didn’t get a response, Elizabeth slowly pushed his shoulders back so he was looking up at her. He still felt a bit fragile, but John looked like himself again. His eyes weren’t a thousand miles away, reliving the trauma, but focused on her.

“Come on, John. We both know you didn’t get any rest on the Daedalus. You gave me the debrief. Everything else can wait until tomorrow.”

After a moment, he stood up. He looked dead on his feet, but Elizabeth wasn’t as worried about him now. She took his hand and tugged him out of the office.

John didn’t say a word the entire walk from her office to his room and neither did she. It was close to three in the morning, so they didn’t meet anyone in the hallways. That was probably for the best—Elizabeth refused to let go of his hand.

When they finally arrived at his door, John activated the sensors and the door slid open. Then he turned back to her.

“Thank you,” he said, almost too quiet for her to hear. He squeezed her hand before releasing it.

“Of course,” she answered, watching him lumber to the bed as the door closed.

When Elizabeth made it back to her room, she was finally able to fall asleep without any trouble at all.