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There were things that didn't make sense to Jamie, after. Things like a ring on a chain around his neck, a kind of metal he had never seen before. Things like his uniform being completely free of the dirt he could have sworn it was covered in before. Things like old aches resolved and new ones replacing them, scars from injuries he had no memory of getting.
Those things would, of course, make sense to him later. Later, when the Doctor came back to get him. Later, when the Time Lords returned his memories to him. Later, when everything had changed.
The Doctor, for the most part, was exactly how Jamie had spent most of their time apart halfway remembering. It would come to him in dreams, wispy and strange, snippets of the exhilaration of running and calm atmospheric humming of rooms he couldn't place. He knew there was someone out there he felt safe with - that he felt himself with - the entire time he was without his memories. Even when he no longer felt like his body was his, he knew there was somewhere else he was supposed to be.
*
When the Time Lords allowed Jamie to return to the TARDIS and the Doctor things were, of course, different - but the important things stayed the same. They could no longer go wherever they pleased amongst the stars, getting mixed up in whatever danger or adventure they felt called to. Instead, Jamie and the Doctor were mostly stuck going wherever the Time Lords told them to.
(Jamie could see the way the restrictions weighed on the Doctor. He was angrier than he used to be, stifled and tired. Jamie wasn't sure how long it had been for the Doctor since they were separated - he completely refused to talk about it - but Jamie could read from the new lines on his face that it hadn't been a short amount of time. Jamie understood, the time had made him angrier too, had filled the gaps of himself he had taken away from him with a fiery sort of exhaustion to keep him warm.)
Some things did stay the same. The Doctor could wring joy and curiosity out of a stone, could find ways to be kind no matter the situation. The TARDIS still took them off course sometimes, still took them spiraling into impromptu adventure, still took them where they were needed. If anything, it was Jamie and the Doctor who had changed more than he'd like to admit, not the situation.
*
Now, months (or whatever the semi-timeless equivalent) after Jamie had been reunited with the Doctor and his own memories, the Doctor is being delicately patient with Jamie.
The Doctor is many things, and has remained those many things through it all, but he didn't used to be so patient. Kind, sure, but he has a tendency to blunder or brute force his way into situations and/or the truth. That tendency didn’t always match up well with patience, not when there was always so much for him to do.
But now, the Doctor spent a long time waiting, and it changed him - no matter how much he refuses to tell Jamie anything about it. It shows in the careful distance he gives Jamie. In the way they don't quite cling to each other the way they used to. The way they don't sleep in the same room anymore. The way they never talk about what their relationship was like before.
The Doctor never forces Jamie's hand, never makes him talk about the odd distance between them. Jamie feels like a ghost, sometimes, haunting his old life. He only really feels himself when the two of them are buried in whatever thrilling adventure they need to focus on. And Jamie loves the Doctor, of course he does, he's just having a hard time fitting in all the pieces of himself in this life now. He doesn't really know what to do with the version of him that has confusing dreams of a face he couldn't recognize and woke up clutching a ring he couldn't remember the origin of.
The two of them don’t even sleep in the same room, the room they used to sleep in before. Jamie isn’t convinced the Doctor is sleeping at all, staying up in the console room long past when Jamie goes to sleep in one of the many rooms the TARDIS offers. Jamie has his things scattered throughout several rooms; his old clothes - all those soft sweaters, button up shirts and kilts - are still stored in their old bedroom, however most of his other possessions are in the TARDIS library, console room and - regrettably - the bedrooms of Polly and Ben. Jamie can’t bear to go into Victoria or Zoe’s old rooms, especially not Zoe’s, but he spends time in his old room and Polly and Ben’s, trying to piece together who he was then with who he is now.
*
Jamie and the Doctor don’t really spend all that much time together anymore. At least not in the domestic down time in the TARDIS, where before they would have been inseparable, bickering over meals in the console room while their friends looked on in exasperation. That’s what makes it kind of odd that the two of them are even together in this moment, the Doctor fiddling with something in the console while Jamie carefully stitches up the edge of one of his kilt’s in the corner where a tear had resulted from snagging against a rock face during their last task.
“Jamie,” the Doctor murmurs from across the room, up to his elbows in a section of wiring, “could you help me for a moment?”
Jamie sets down his stitching without a second’s hesitation. Time and distance may have changed a lot between them, but it could never have stopped Jamie from coming running as soon as the Doctor asked for help.
The Doctor was pointing at loose wiring, asking Jamie to reach into the console to grab hold of a mechanical piece that must have rolled past where the Doctor could reach with his hands full.
Jamie rolls up his sweater sleeves, ready to reach in when the Doctor stops him with a gasp.
Jamie pulls his hands back, afraid all at once that he’d touched the wrong thing and somehow hurt the TARDIS, when the Doctor grabs both arms, pulling them out so he can inspect his forearms.
“Jamie? Did something happen?”
Jamie shook his head.
“Jamie?” The Doctor is visibly struggling to find the words for what to say, still holding Jamie’s arm gently. It’s not often that the Doctor is at a loss for words. It’s unsettling to Jamie, even now when so much about his life has been unsettling for so long. “Jamie? What happened? What did you do?”
Jamie could tug his arm away from the Doctor with almost no issue, he knows. He’s always been the brawn, been stronger than the Doctor in the physical sense. He lets the Doctor hold on.
Jamie stares at the TARDIS console instead of at the Doctor’s face. “We were married before, weren’ we?”
“What? Of course we were. Why?”
Tears gather in Jamie’s eyes unbidden.
“Are we still married now?”
The Doctor makes a wounded noise in the back of his throat, like he’s suffered a physical blow. He pulls Jamie against him gently, tucking his face into the side of Jamie’s neck, the closest he’s physically been to Jamie outside of the rush of a dangerous mission since they were returned to each other.
“Of course we are”, he whispers into the side of Jamie’s neck where he has tucked his head. “If you still want to be, of course we are”.
Jamie nods his head in return and clings onto the back of the Doctor’s familiar ratty old coat as hard as he can with the arm the Doctor isn’t still cradling softly between them - a position so familiar Jamie thinks he may have dreamed about it in detail, even if he didn’t remember what he was dreaming of.
*
In the time that the Doctor and Jamie were separated, Jamie struggled.
He remembered it like a bad dream, twisted and now foggy with distance.
He felt odd and separate from his body, he had scars he didn’t recognize the origin of, there was something missing, and the confusion and lingering grief that didn’t make any sense hurt.
That hurt was why he did it in the end, why he took to carving new scars into his arms. It felt a little silly at the time, still does now, and it didn’t particularly help, but Jamie didn’t know what else to do, not when he felt as alone as he did.
*
The Doctor pulls them to their old bedroom, and carefully coaxes Jamie into lying down with him so they can curl around each other.
The Doctor clears his throat in the tenuous silence.
“Jamie? Could you please tell me what happened?”
The Doctor is running his thumbs back and forth across Jamie’s forearms, and Jamie feels a little mesmerized and strangely soothed, caught by the repetitive motion.
“Nothing - nothing made any sense,” a shuddering breath escapes Jamie’s chest, “It didn’t feel right, when they sent me back. Nothing made any sense.”
Jamie feels the Doctor tense against him at the mention of the Time Lord’s memory wipe, but he doesn't interrupt or otherwise tell Jamie to stop.
“I had your ring and I had clothes that were too clean to be from the middle of a battle and I had scars that I had no memory of ever getting. I knew something was missing but I didn’t know what it was. I didnae feel like myself anymore and I thought maybe … maybe the new scars would make me feel like myself again, would make everything make sense”.
Jamie has never seen the Doctor cry before - there are parts of his mask that he doesn't drop for anyone, not even his husband - and he doesn’t technically see it now as the Doctor tucks his whole face into Jamie’s chest. The only real show of distress or the Doctor's that Jamie can feel is his tandem heartbeats thumping fast and heavy against Jamie’s chest.
“Oh Jamie” the Doctor whispers without lifting his head. “I’m so sorry. I’m so so sorry”.
Jamie lifts his hand to the Doctor’s shaggy head of hair, running his fingers through it gently.
“It’s not your fault. I love you, I really do. It’s not your fault”.
The two of them fall asleep like that, together in their old bedroom. When Jamie wakes up the Doctor is still tucked against him, breathing deeply.
So much happened in their time apart, but the Doctor’s face remained the same, and how deeply they loved each other too. In the glowing light of the TARDIS, in their bedroom and in their home, Jamie lets himself feel more hope than he has in a long, long time. Maybe, things are starting to make sense again, and the two of them can make everything make sense, together again.