I may be coming back to this fandom, it helps that Into Darkness was so epic.
Just a simple stand alone oneshot to start, so there are spoilers- it's a minor deleted scene/what-if.
He stays completely still as he comes back to conciousness, and partially revises his opinion of the Vulcan. The alien would break a bone, and if pushed he could break several.
He can feel the restraints holding him down, unfortunately, while he is better at everything, it would take him a while to escape the unfamiliar restraints, and he'd probably trip an alert and end up drugged before he can take his revenge.
He drags up memories of what happened, the loss of his crew- damn that Vulcan, he lied- his attempts at running to fight again another day, and the stubborn alien that had chased him, and had even sent him such strong, almost crippling emotions underneath the disorienting mental attack.
The woman that beamed down, the lieutenant who slipped and revealed her captain's identity, had tried stunning him, and the alien's subsequent attack- far more brutal than his captain's, and far more effective- left him dazed. She had yelled something, something about Kirk.
He can hear the grumbling of the doctor, and warily cracks open an eye. There's a machine, taking his blood, and he gets a quick glimpse of an all too still figure. He quickly closes his eye as he hears a door hiss open.
"Doctor, what is the Captain's status?" The Vulcan asks, and Khan begins to plan his death.
"He's alive when he should be dead, it'll take time to see the effects . . . He was severely irradiated after fixing the core."
Core . . . Did Kirk actually go into the warp core to stop his ship from falling? Khan's reluctant respect (Because Kirk would do anything for his crew, because Kirk knew not to trust him when even Marcus had foolishly thought that unfreezing Khan had given him the right to order him around, because Kirk wouldn't have killed Khan's crew like the Vulcan had) goes up a notch.
"And Khan and his crew?"
The question almost makes him jolt, demand answers.
His crew . . . still alive?
"Once this transfer is complete, I'll put Khan in a deeper coma- the cryo-pods are all stable, not even badly jarred." The two talk a little longer, and Khan gives in to temptation and cracks open his other eye, spotting the pods- all of them. His control slips and he opens both eyes to stare at the pods, intact, not blown up.
Alive.
"You're awake." The Vulcan notices and the Doctor swears.
"You didn't kill them." Khan is too tired, too relieved, to engage the other in a mind game. "Why?"
Because as agonizing as it had been, first having his crew held as collateral, then used against him, it had been an effective strategy- He had made mistakes, many mistakes, the least being not blowing up the Enterprise.
"I believe the Captain would say, because we are not like you." The alien's response is cold, detached. The Doctor hovers in the background.
"You said you didn't lie."
"I said the torpedoes were yours, you assumed your crew was still in them." Khan wants to laugh, because both Vulcan and Human have managed to defeat him and it has been so long since he's had a worthy opponent . . . admitting defeat isn't even painful because his crew is alive.
"What will happen to them?"
"They will remain frozen. From what I understand from the admirality, John Harrison will be listed as killed, and if you cooperate, you will be frozen as well."
It's the only option, really, John Harrison did die, and Khan has no intention of ever obeying Starfleet again, and he's not so sure their prisons would hold him for long, or whatever 'humane' method of death- if his blood is being used to bring Kirk back from death- would even kill him.
"You have my permission to use my blood to save your captain. It worked on a little girl in a coma." He hear's the doctor's hiss and the Vulcan seems to stiffen. He's done talking, and turns to focus back on his crew.
It's a fair trade, he thinks days later, as he is injected with the nessecary drugs to survive being frozen, the Captain of the Enterprise for his crew.
Might do a couple more chapters with different characters . . . Spock and McCoy definitely, Dr. Marcus, Scotty and Kirk maybe. Might even do a second drabble on Khan at somepoint.
Short of an explosion, I don't think there's much that could kill Khan, and I imagine that strapping a bomb to someone to execute them in the future would be highly frowned upon. It's frowned upon now, on that note.