Kirk dies, and there's nothing Bones can do about it.
Spock killed that damn sonofabitch Kahn before he even had the idea of using Kahn's blood to make him live, so Kirk stays dead, is what's worst about it. He stays dead, and he said that he'd never leave Bones to face the horrors or space alone, and Jim Kirk never broke a promise if he could help it.
So Bones decides to help him keep it.
It's not that hard to steal Jim's body away, really. No one questioned the grieving doctor Bones presented when he asked to be left alone, just like no one questioned him when he wanted access to the cryotubes, when he changed the count back to the original number after he managed to take one. His plan might require some ... bending of the Hippocratic Oath, but Bones figures that even if he spends the rest of his life in jail, it'll be worth it as long as Jim is alive.
Bones misses Kirk's funeral. It was closed-casket, the body of the superhuman he'd warmed up then shot provided the weight. Jim's will had requested closed-casket specifically. He had told Bones why, once, after too many shots of Alderian whiskey and before the first kiss of many they were to share, back in their Academy days, back when the hardest challenge either of them had to face were the looming exams.
"Ya know," Jim had said, half-draped over Bones. Physical space had long stopped existing between the two of them. "Ya know, I should probably change my will."
Bones hadn't thought much of the topic at the time. "What on God's green Earth brought this up?"
"Well," Jim had replied, staring at the glass in his hand, "I was thinking, about the future. And how I used to think I'd die bloody, from a fistfight or bike crash or somethin' like that. And no one would find me for a few days, so I figured that by the time I'd be found I wouldn't look all pretty like I do now."
Jim had taken another sip of whiskey, then. "Shut up, that's not the point. Anyway, because I thought I wouldn't look too good, and the only people who would've seen me would be the undertaker or something, because Mom, you can't convince Mom to come back to Earth if you have the entire Antican diplomatic team, and my brother wouldn't get the notification until too late, so I figured I'd just be buried with the lid closed, you know?" Then Jim had set down the glass, and pulled Bones to him. He still remembered the stink of alcohol on Jim's breath, the buzzing in his own fingers.
"But now," Jim had said, "Now I've got you. And I know you would come and see me if I died. Wouldn'tya Bonesy? Wouldn't you come to see me if I died?"
And Bones had said yes, of course he would, of course he would come to Jim's funeral.
Bones doesn't come anyway. He figures that it's not really Jim's funeral, goddamnit, because Jim is coming back.
People notice, eventually, when McCoy stops showing up to events. At first, it's just little things, like Sulu's fifth anniversary party. But more and more often, Bones skips his shifts, puts off his duties, to spend more and more time staring at Jim's body in cryosleep, begging the new serums to work. It's not until a patient dies when he wouldn't tend to them that Captain Spock is forced to step in.
"You don't understand!" Bones growls. "I couldn't leave Jim! He needs me, dammit, more than Ensign Roe did!"
"Ensign Roe died because you were not there to administer the proper medical care. Jim is dead, Doctor. You need to accept this."
McCoy makes a run for it not long after that, stealing a supply shuttle and heading out into the emptiness he once abhorred. There are no days for him, no nights, only short periods of rest, and evermore attempts to revive Kirk. But Jim's body is decaying, slowly but surely, each time he is warmed up to test the serums. If this final test doesn't work, Bones won't have anything left. He'll probably just kill himself, he figures, just turn on the self destruct and go out with a bang.
The last test with the superhuman serum is the most fraught Bones has ever been. His fingers shake as he injects it into Jim's cold, softening body.
"Please," he whispers, "Please live."
It's hours later when Bones wakes. The soft beeping of the stolen medical equipment fills the shuttle, and Bones wants to weep with joy.
It's a heartbeat.
Jim is alive.
Jim will live.