All standard author's notes and disclaimers apply.
Special author's note: according to my research, permanent/serious brain damage sets in 3-5 minutes without oxygen and it becomes increasingly unlikely that the patient can be revived at all. To me, it seemed like Kirk must have been dead at least four minutes and probably closer to ten or more by the time they would have gotten him into stasis. I beg pardon for not being able to remember who else was in the infirmary with McCoy- I've only seen the movie once.
Too Late
Bones stared down at the body laying on the gurney- nothing more than an empty shell now. The features had been well-known to him for years, but he had difficulty reconciling the face as one that should be familiar. Without life, it was almost unrecognizable. This wasn't James T. Kirk. Kirk would never be so still, so unanimated, so... empty. Bones hadn't really believed it when he was told that their venerable captain was dead- if asked, Bones would have said that Kirk didn't know how to die- but nothing could make it more clear that James Tiberius Kirk was indeed gone than seeing his body.
Anger and grief vied for dominance in an unceasing dance within McCoy, and the struggle took all strength from him. He didn't have the luxury of breaking down or experiencing the full emotions that would later drive him to the bottle; people were still hurt, still dying, still needed his attention. He could take a moment and only a moment right now to grieve for his lost friend.
Suddenly, the tribble on the table- once dead- made a noise and began to undulate with life. Adrenaline flooded through McCoy as he realized what Khan's blood was capable of, that it might be enough to bring back Kirk. He began issuing orders at warpspeed to the other doctors and nurses in the room, only to stop himself mid-sentence when reality set in and swiftly destroyed the spark of hope that had taken him.
"Sir?" one of his aids called, uncertain what to do.
Bones stood motionless, his face drawn and pale as he apologetically stared at Jim's lifeless face, silently begging for forgiveness. "It's too late..." he whispered to no one in particular. "Four minutes without oxygen and permanent brain damage begins to occur, worsening the longer the brain goes without oxygen. It's too late..." he repeated.
"We can bring him back-" the aid objected, but Bones interrupted him, shaking his head.
"We might be able to revive him," the doctor corrected somberly, "but it would be a miracle if he was anything more than a vegetable. He'd never be the same. Jim Kirk wouldn't want to live that way."
It wasn't just his opinion as a friend or what he'd been told in confidence; like everyone else on the Enterprise, Kirk had a living will stipulating what measures could be taken to save him and under what circumstances he would rather die.
"Just let me go."
Jim had spoken those words years ago, without hesitation or gravity in a flurry of statements, but they resonated very differently to Bones now. The mild sense of apprehension that accompanied the hope that such an order would never have to be carried out was now met with the horror that it had, and he felt the past and future connected as if by a straight line with nothing between. The future had become the past, and the past had become the future.
Bones walked over to the gurney were Kirk's body lay- just a shell- and tears slipped from his eyes as he stared at the face that should have been familiar but was almost unrecognizable. "I'm sorry."
Bones knew he would be saying that for as long as he lived, in the quiet hours of the night and the moments when no one was looking... but Jim Kirk would never hear.