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There's a good reason this timeline is an alternate, Captain, you just haven't thought of it yet

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It takes about a week for the Enterprise to limp back to Earth, stopping along the way to replace the warp core and repair enough that they make it back in mostly one piece.

It isn’t exactly a relaxing week. The only real rest Leonard gets is four hours of forced sleep after he finishes his operation on Pike, which takes thirteen grueling hours. Then he’s on to triple shifts, napping in his office between patients whenever he can, shovelling food into his mouth only because he knows his body needs fuel to run on.

He sees Jim three times. Twice when he comes to check on Pike after the surgery. And once in passing in the corridor, his head bent towards Spock’s as they discuss something in low, urgent tones. His eyes meet Leonard’s and he nods as Spock intones a level, “Doctor McCoy,” and then they’re gone.

Leonard doesn’t give it a second thought. It doesn’t even occur to him that something might be wrong, because, well, everything’s wrong, and there’s no time to worry about personal issues when he’s alternating between healing physical pain of the steady trickle of crew and Vulcan’s who pass through his doors, and playing psychologist in an attempt to minimise the mental anguish of what they’ve just been through, the things they’ve witnessed, the people they’ve lost.

He’s so busy helping everyone else grieve that it doesn’t even occur to him that he’s lost anything. Because he knows Jim is safe, and Earth is safe, and that’s all that matters.

When they get back to Earth there are endless debriefings. Leonard is made to justify every medical choice he made, as if he’s a second year medical student rather than an experienced doctor who, admittedly, has never been CMO of a starship, but who ran a trauma unit as head surgeon for years. He tries not to take it personally. He knows every other senior crew member is being made to do the same thing, and he wonders how many coals Jim is being raked over.

When the meetings are done each day, he goes to the cafeteria of the building they’re all being housed in temporarily. He’s relieved, in an odd way, that they haven’t been sent back to their dorm rooms, to walk down hallways that would have been once filled with fellow cadets whose bodies are now floating in space, waiting for the main fleet to show up and collect them.

He eats alone the first night, but then one by one other crew members show up. They join him wordlessly, and sometimes they eat in silence and sometimes they talk. As the days go on, more and more of them show up, and somewhere along the way Leonard thinks that maybe it’s his duty to keep their spirits buoyed, to keep some semblance of normalcy, so he grumbles at them to eat healthier and makes them share stories of their families and childhoods, and pretends that this isn’t the job of the captain or first officer, both of whom are conspicuously absent.

Leonard thinks maybe he understands why Jim doesn’t show up. He’s in more meetings than the rest of them combined, and it has to be exhausting. He also knows that Jim is really good at putting on a brave face, but sometimes the mask he wears starts to crack and he can’t always pull himself together. So he understands the avoidance of the crew. What he doesn’t understand is why Jim is avoiding him .

It’s a few days of waiting for Jim to let himself into his room – Leonard had messaged him with the entry code the minute he’d gotten his temporary room assignment, and had expected Jim to do the same – before he starts sending Jim message after message, asking what’s going on.

He doesn’t get a response.

On the fifth day he stomps down to Jim’s room after he knows the debriefings are long over for the day. He’s pleased to discover that his medical override works even here, and so he lets himself in.

Jim is not there. In fact, it doesn’t look like Jim has ever been there.

Leonard considers waiting, but he has a sneaking suspicion of where Jim might be. So he asks the computer to locate Spock’s room, and stomps down there instead.

Spock answers the door, and doesn’t seem surprised to see him. He lets Leonard in, and there, sitting at the table in front of a plate of uneaten food, is Jim.

He looks exhausted, and Leonard longs to reach for him, to smooth his hands along the tense lines of Jim’s shoulders, to press a reassuring kiss to his temple, to wrap his arms around him and tell him it’s going to be okay.

Two weeks ago, he would have done it without hesitation, Spock’s presence be damned.

Two weeks ago, he thinks Jim would have welcomed it, as he always had.

But now...now he’s not so sure.

Jim doesn’t even look at him, and suddenly Leonard is furious in a way he hasn’t been since he confronted Spock about his idiotic decision to kick Jim off the ship.

“Great,” Leonard says hotly. “So you are alive. Just checking.”

Jim lifts his head, and he’s so shut down, so withdrawn, than for a moment it’s like Leonard is looking at a stranger. And then it occurs to him that he has that switched. He’s the stranger. Jim is closing off like he doesn’t know him, and that makes his heart ache and his fists clench.

“Eat your fucking meal,” he says. “That’s an order. I’m still your doctor, at least.”

Jim flinches on the word ‘still’ and that’s everything Leonard needs to know about what Jim is doing. Cutting him off, shutting him out, breaking up with him without saying a word.

“And when you’re ready to talk to me and tell me what the fuck is going on, you know where to find me.”

Leonard stalks to the door, and is halfway down the corridor before Spock catches up with him. He stops, only because he knows Spock can easily outpace him, and can probably override any door Leonard would try and hide behind.

“I don’t have anything to say to you,” he says, and Spock regards him quietly. There’s something uncomfortable about Spock’s gaze, like Leonard is under a microscope being dissected slowly. Like Spock is searching for something. There’s a softness to his expression that makes Leonard even angrier. He doesn’t need the Vulcan to look at him that way. Doesn’t want it.

Spock reaches a hand out towards him, and Leonard reacts without thinking, stepping back, knocking the arm away.

“Don’t put your fucking hands on me,” Leonard hisses, and he doesn’t know why he’s so angry at Spock – besides the obvious of course, but if Jim can forgive all of that, then it’s not Leonard’s place to hold a grudge, especially now that he and Jim aren’t…

Anything, maybe.

“My apologies, Doctor,” Spock says. His hands are behind his back now, his expression bland and unreadable.

“Just...look after him for me,” Leonard says, and this time when he walks away, Spock doesn’t follow.

~~~

At the end of the week, they’re cleared to go back to their dorms, and it’s as horrific as Leonard had expected. Someone has been in and removed his roommate’s belongings, packaged them up and shipped them back to Wyoming to his grieving mother and sister. Leonard hates that he doesn’t even know what ship he was on, and tries not to think about how it could have so easily been him, if not for a dozen or more what-ifs.

In the half of the room which is cluttered with things, Leonard takes stock of how many belong to Jim. There’s a pair of his boots under the bed, a book he’d been reading on the nightstand, a shirt Leonard had borrowed just because it smelled like him hanging over the desk chair.

It makes Leonard regret never letting Jim hack into the room allocations to get them a place together, like he’d been threatening to do since first year. Leonard had worried it would put too much pressure on their blossoming relationship, would make it too hard to watch Jim warp off into space after graduation while he stayed behind.

Now it all feels like wasted time.

He wonders if Jim’s roommate survived, or if in the building next door Jim is looking around a half empty room in the same way Leonard is.

Classes do not resume, so that is one small mercy. Instead everyone is given time to go home if they want, to meet with counselors and find comfort in each other.

Leonard signs up for as many shifts at the hospital as they’ll let him take. He’s grateful that no one argues. He’s not exactly friends with any of his colleagues – Leonard doesn’t really do the whole friendship thing, except with Jim, and that had passed from friends to something much more in the face of a few short months, so he’s not entirely sure he even knows how to be friends with someone – but their presence is comforting. Normal. Safe.

His meal times become erratic, fitting in around work, and yet somehow the rest of the crew who he’d eaten with the week before find him anyway. It’s not just cadets, listless without anything to do, but actual ensigns and lieutenants, who surely have better places to be than in the Academy cafeteria, listening to Leonard grumble about idiot junior doctors who can’t follow basic instructions.

Jim still doesn’t show up, and when he finds a way to delicately ask, it becomes clear that Leonard is the only one Jim is avoiding. He’s gone room to room, door to door, all week, checking on his crew, making sure they’re safe. It makes sense – people do drastic things after facing such tragedy. And Leonard wonders how bad he’ll have to get before Jim shows up at his door.

He finds out a few days later. It’s been a particularly bad day – a kid had died on his table, and the loss at being unable to save him hit Leonard in a way that he hadn’t felt in years. In the kid’s face he saw everyone who should still be walking around campus, worrying about finals, every injured person who’d been rushed into sickbay too late to be saved.

Leonard had been quiet at dinner, letting Uhura take over his role of keeping everyone talking. He’d listened to them talk, hardly paying attention, definitely not joining in.  

He doesn’t even remember what it was that made his head snap up, made the words fall from his lips.

“It doesn’t matter,” he’d said, and everyone had stopped talking. Everyone had stared. “It doesn’t matter what we do, because this is just an interlude until they ship us all back out there just to watch us die in space. Just like all of the others did.”

“McCoy–”

Leonard hadn’t even stopped to see who was talking to him. He’d just stood up, leaving his tray where it is amidst the stony silence of his crew, his peers, his...friends, perhaps. And he’d left.

He’s in his quarters, with the absence of his roommate weighing on him like someone had turned up the anti-grav, and contemplating which alcohol would be best to drown his sorrows, when Jim shows up.

It’s stupid, but it gives Leonard a glimmer of hope that he doesn’t knock, just lets himself in.

“Who called you?”

Jim slides easily into the seat across from Leonard, like he’s done hundreds of times before.

“Everyone,” Jim says, and he can’t keep the surprise out of his voice. “They’re all worried about you.”

“It’s nice to know they care,” Leonard says pointedly, but it actually feels...pleasant. The way family would be, if he had a family who gave a shit about him.

“You know I care, too.”

Leonard leans back in his chair. “You have a funny way of showing it.”

Jim won’t meet his eyes. “I’ve been busy,” he says, which isn’t a lie, but it isn’t the whole truth either. “I didn’t want to bother you.”

“Sure,” Leonard says with a shrug. “I can see how you’d think letting your boyfriend know you’re okay would be a bother.”

Jim’s face pulls taut, guarded, and Leonard sighs.

“I know, I know,” he says. “Don’t worry, I picked up on all of the hints loud and clear. You want to break up.”

“I don’t want to,” Jim says, and there’s a pause long enough to give Leonard a minute amount of hope before it’s ripped away again. “But we have to. It’s the right thing to do.”

Leonard’s brows shoot up. “Care to enlighten me on why, exactly?”

Jim shrugs, looks away. “Spock…”

Leonard feels like all of the air has been sucked out of the room. It takes him a while to pull enough oxygen into his lungs to speak again.

“So,” he says. “You and Spock are...friends now.”

Jim gives him an odd look. “We are,” he says, and Leonard feels his face twist in anguish, sees the answering panic on Jim’s face. “We’re not – no. Bones. Not like that. I just...I respect him a lot. I trust him. But it’s just friendship.”

“And your new friend doesn’t like that you have a boyfriend?” Leonard asks. It doesn’t make any more sense out loud than inside his head, and it makes Jim frown at him for a long moment.

“No. Not at all. I just...I owe him. And I don’t want to hurt him.”

“But it’s okay to hurt me?”

“Sometimes you have to hurt people now, so that in the long run they’re happy,” Jim says, and Leonard shakes his head slowly.

“Jim,” he says. “Kid. You’re not making any sense. I’m trying my best not to leap out of my chair and shake you by the shoulders, or punch you, or kiss you right now.”

Jim makes a pained noise in the back of his throat, looks away.

“But you’ve got to tell me what’s going on. You owe me that.”

Jim stands up suddenly, and Leonard thinks he’s going to leave. Instead he walks over to the window and stares out.

“When I met Ambassador Spock,” Jim begins, “he did this...mind meld thing with me. Showed me who he was, so I’d trust him. He was careful not to show me too much, not to give me any information about the future – in the other universe, I mean – but there was plenty of stuff that bled through.”

Leonard sits silently, waiting, and when he doesn’t interrupt, Jim continues.

“I saw them, the crew on the other Enterprise. I saw them all together. And I saw you a lot. I thought maybe it was because, you know, you’re always in my thoughts, but then a word came into my head. I had to ask Spock about it later. T’hy’la.”

“I don’t know what that means,” Leonard says, and Jim grimaces.

“Friend. Brother. Lover... Soulmate. You’re Spock’s T’hy’la, Bones. In that other place, where almost everything else is the same. You’re soulbonded to each other. And I saw how, I saw why. First by necessity, and then through love. If there’s such a thing as soulmates, you’re each others.”

Leonard laughs, because Jim has to  be joking. But when Jim doesn’t join in, it dies in the back of his throat and he swallows it down.

“Jim’ he says. “You’re not making any sense.”

“I asked the Ambassador about it,” Jim tells him. “He was reluctant to tell me at first, but I pushed and pushed until he admitted that it was true. You’re Spock’s soulmate. And he’s yours. And I can’t stand in the way of either of you being happy.”

Leonard can’t stop staring at Jim like he’s gone insane. “Jim,” he says, patiently as if talking to a very young child. “Spock is not my soulmate. I don’t love him. I don’t even like him. Hell, I don’t even know him.”

“Yet.”

Leonard rolls his eyes. “We’ve had maybe a handful of conversations, and every one has resulted in us snapping and yelling at each other. I hardly think that’s going to lead to some romantic soul bonding bullshit.”

Jim grimaces. “What I saw in Ambassador Spock’s head...I got the impression that you both liked arguing. That it was almost...foreplay for you both.”

Leonard’s gut twists.

“Well, thank you for ruining my day even further with that mental image,” he says. “Which only goes to show how wrong you are. Ambassador Spock is not our – your – this universe’s Spock. And I am not that Doctor McCoy. They’ve lived different lives, Jim. They’re different people.”

“How do you know?”

Leonard doesn’t have an answer to that, but he does know something. “Because I don’t believe in soulmates,” he says simply. “I would never agree to a soulbond with anyone. And because if I did have a soulmate, I think it’s pretty obvious to us both that it’d be you.”

He stands up and walks towards Jim. Jim’s hands are hanging limply by his sides and he grasps them.

“I don’t know why, but I love you, Jim Kirk,” Leonard says. “Enough that even after all of the shit you’ve put me through these past few weeks, I still want to feel your arms around me. Enough that the booming voice of God could split open the roof above us and yell at me that Spock’s my soulmate and I wouldn’t care. Because I choose you, you idiot.”

Leonard moves in to kiss him, but Jim leans back.

“But Spock,” Jim protests.

“I don’t want Spock,” Leonard says, exasperated. “Do I need to get it tattooed across my forehead? Why aren’t you listening to me?”

Jim frowns. “But what if Spock wants you?”

“Ignoring the fact that I get a say in the matter, and I don’t give a flying fuck whether Spock wants me or not,” Leonard begins, then fishes his communicator out of his pocket. Before Jim can stop him, he flips it open and calls Spock.

“Doctor?” Spock’s tone is full of surprise, but also a warmth that has never been there before.

“Jim thinks we’re soulmates,” Leonard says without preamble. “Because we are in another universe. And I think that’s a crock, that we’re not the same people they are, that our destinies are infinitely different.”

There’s a long pause. “I must concur with you, Doctor,” Spock says, and Leonard searches for any hint of disappointment in his voice, but finds none. “I do not think such things are predetermined, but are instead shaped by our experiences. From the little that Ambassador Spock has revealed to me, our experiences have diverged significantly from those in the alternate timeline, and thus have resulted in many differences.”

“So you don’t think we’re soulmates,” Leonard prompts.

“I do not,” Spock answers.

“And you’re not sitting around wistfully wishing for a romantic relationship with me?”

“I am not,” Spock replies again. “While I respect you as a doctor, and for the care you have shown to our crew, and your appearance is pleasing to the eye, I do not wish to engage in romantic or sexual situations with you.”

“Plus, Uhura is considerably hotter than me,” Leonard says, and there’s a huffing noise that he thinks may be Spock suppressing a laugh.

“Quite,” Spock says.

“Well,” Leonard says. “That’s sorted. Not soulmates in the slightest.”

He feels Jim’s body relax, leaning in against him.

“If that is all, Doctor,” Spock says, “I have tasks to attend to.”

“That’s all,” Leonard says, then, “except – Spock, I suspect that whenever we’re in close quarters together in the future, you and I will spend a considerable amount of time arguing.”

“Previous experience does suggest this to be the case,” Spock agrees easily.

“I just want to make it clear that any such arguments are in no way to be construed as flirting or foreplay,” Leonard says firmly, ignoring the way Jim presses his lips together, as if trying not to laugh. “Please interpret any such interactions as annoyance and exasperation and, I suspect although it pains me, grudging respect.”

“I will make a note of that,” Spock says, sounding somewhat baffled, then bids him goodnight and terminates the connection.

Bones drops his communicator back into his pocket and raises a brow at Jim.

“Are you convinced?”

“Yes, but–”

“And do you feel like an idiot?”

“Yes, but–”

“And are you going to apologise?”

“Yes, but–”

Leonard opens his mouth again, but Jim’s hand slaps across it.

“Spock’s wrong,” Jim says, and Leonard pulls away from Jim’s touch, annoyance flaring in him. He starts to mutter about stupid boneheaded Kirks, but Jim talks over him.

“You are way, way hotter than Uhura,” Jim says, and Leonard stops talking. “But don’t tell her I said that.”

Leonard rolls his eyes. “Do you think you’re going to get off the hook that easily? That you decide to end our relationship – without talking to me, without even telling me – because of some idiotic idea, that you abandon me for almost three weeks and don’t even let me know you’re safe and uninjured and as sane as can be expected, that you argue with me when I try to tell you that if I have a soulmate it’s you, not that pointy eared Vulcan, and then I’m going to forgive all of it just because you pay me a compliment?”

Jim looks at him for a long moment, face serious. Then it cracks into a grin.

“Yes,” he says, and kisses Leonard.

And, goddamn him, he’s right.