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It was stupid, just plain stupid. You were being ridiculous, you knew you had to be. He wouldn't care if you told him, he was an alien who traveled through both time and space after all, it probably wouldn't even matter to him! Then you remembered what had happened the other time, along with what he did when he was furious, and you kept quiet.
It terrified you, possibly ending up on the receiving end of the Doctor's fury for telling him, it shook you to your very core. While you logically knew it was unlikely for the Doctor to actually go off on you, you'd seen his rage briefly be aimed at Martha twice, so it was still possible. Your heart still ached when you thought about how you had comforted Martha when she'd confided in you about being scared of the Doctor those two times. It made it so much harder to be honest with him.
But, you had to tell him! You'd been traveling with him for a good while now, he deserved to know the truth. Plus, with you technically having been in the closet for so long, you just wanted to come out to someone without it going to absolute sh-
"You alright?"
You nearly lept out of your skin at the sudden voice, breaking you from your thoughts and causing you to look up. The Doctor stood at the TARDIS's console, gazing at you with an expectant expression, and you realized he'd been talking to you. "Um, sorry. What did you say?"
The Time Lord frowned slightly, then moved away from the console and approached you. "I asked if you were alright. You've been out of it for a little while and wanted to know if something was bothering you."
A pit formed in your stomach, your fears returning as you looked away from him. Something was bothering you, and you wanted to tell him so badly. But, it could end horribly if you did. You couldn't bear the thought of facing his rage.
"...Do you wanna leave?"
Your head snapped in the Doctor's direction, jaw nearly hitting the floor. "Wh-what!?" you gasped, shocked by the question.
"It's alright if you do wanna leave," the Time Lord told you, looking sad but understanding. "After everything with the Master, makes sense that you'd want to go home-"
"No!" you shouted, jumping to your feet. "No! No! No! No! I don't want to leave at all!" a bitter laugh burst past your lips. "Besides, what home would I even go back to? Unless you count the streets or that one abandoned building I sometimes took shelter in."
You slapped a hand over your mouth when you realized what you'd said, but you could see that the damage had already been done. The Doctor was staring at you, eyes wide with shock and mild horror. "You were homeless when we met? For how long?"
"...When we first met...just over four years," you sighed. "Been on the streets since I was fourteen."
A heartbroken expression took over the Doctor's face, and you felt your chest grow tight with emotion the longer you looked at it. "Why?" he asked, voice strained with all the thoughts going through his head. "What happened that left you without a home?"
Unable to meet his gaze any longer, you dipped your head down and slumped back into the chair by the TARDIS's console. It was time to bite the bullet. "Well, let's just say my parents weren't very pleased when I came out to them as non-binary and pansexual," you involuntarily barked out another bitter laugh. "They screamed at me, called me so many homophobic and transphobic names, told me I was going to burn in Hell for being "wrong", and then literally threw me out with nothing but the clothes on my back."
Tears soaked your face and blurred your vision, so you quickly wiped them away the best you could. Just the mention of that fateful day caused it to replay in your mind, your chest and throat tightening in response. Quiet sobs escaped your mouth, being the only noise over the eerily deafening silence that had fallen over the TARDIS.
"WHAT!?"
You let out a startled yelp, head snapping up to see the Time Lord pacing furiously around the room and angrily running his fingers through his unruly hair. For a brief moment - with just the sight of his rage - you were terrified that the day with your parents was about to repeat itself, believing you were about to be the next target of the rage that came from the creature you had trusted most.
But then, you heard what he was saying.
"What the- How could they- What kind of parents would do such a thing!? Since when was being LGBT seen as a guarantee to get into Hell, if it even exists at all. I know Gay Marriage wasn't legal yet, that unfortunately won't happen until 2014, but queer couples were still seen as acceptable. Same with having a different gender identity!" He suddenly whirled around and approached you, making you flinch the tiniest bit. Once he was close enough, your closest friend crouched down slightly to your level and placed firm but comforting hands on your shoulders, then gave a reassuring smile. "You're not "wrong", there is absolutely nothing wrong with you. It's okay to not see yourself as the gender you were assigned at birth, and it's perfectly alright to be gender-blind with who you love. Hell, I'm pan myself."
You blinked several times, the out-of-nowhere revelation taking you aback. "You...you are?" you questioned, voice barely above a whisper, wanting to make sure you hadn't misheard him.
"Well, technically panromantic grey-asexual would be more precise, since I've never really had any sort of interest in sex at all but have definitely been in love before. Ah, but that's besides the point!" he shook his head and firmly met your gaze again. "Your parents were the wrong ones, not you. You're on the right track because you were born this way, and no mistakes were made because God- no, hold on," he paused for a moment, seemingly to think about something. "...Sorry, that's "Born This Way" from Lady Gaga. The point still stands though! You're perfect just the way you are, and you are not alone, (Name)."
There was a long moment of silence, neither of you speaking or breaking eye contact. Then, tears of both relief and happiness began to stream down your face as you began to sob loudly, arms wrapping around yourself. The Doctor's hands left your shoulders and instead wrapped around your waist, pulling you close. You instinctively buried your face into his chest, finally releasing all the pent-up emotions you've held in for so long.
As you broke down in the Doctor's arms, the steady beating of his two hearts filled your ears and reverberated in your head. It was in that moment that your heart and soul warmed, and you knew you'd never feel safer with anyone else ever again. You felt safest with the Doctor and the Doctor alone.