A/N: I know nothing about Star Trek except what's in Into Darkness I'm sorry I'm so so sorry for the horrible canon lapses that are probably there. Also probably sequel coming sometime! Tell me what you think! :D

"I'm going to make this very simple for you."

"Captain!"

His first thought is of his captain, oh what sentiment, especially for one calling himself a Vulcan. What disdain I used to feel for that word, and how dependent I've become on the blasted thing itself… "Your crew…for my crew." No, you idiot, don't hesitate.

"You betrayed us."

And I thought people would become at least slightly more intelligent in whatever century this is. No such luck, no rest for the weary. "Oh, you are smart, Mr. Spock."

"Spock! Don't – " Khan struck Kirk's head with the butt of the gun and he collapsed to the floor with a cry. Another useless idiot in a world of useless idiots. More than one world, now. Why must they multiply?

An image leaped into his head unbidden – happy and laughing, so long ago with –

"Mr. Spock." Long-suppressed emotion flashed briefly on Khan's face, giving his demand an air of desperation. He blinked back tears. "Give me my crew."

"And what will you do when you get them?"

"Continue the work we were doing before we were banished."

"Which as I understand it involves the mass genocide of any being you find to be less than superior."

Don't answer that, hard to contain emotions. "Shall I destroy you, Mr. Spock?" And Khan would. He was very, very prepared to do so. Worth it, all worth it. He will understand. "Or will you give me what I want?" Khan didn't want to. But he would.

"We have no transporter capabilities."

He could hardly suppress his disdain at this Vulcan's stating the obvious. "Fortunately, mine are perfectly functional. Drop. Your. Shields."

"If I do so, I have no guarantee that you will not destroy the Enterprise."

He was really beginning to hate him. "Well, let's play this out logically, then, Mr. Spock. Firstly, I will kill your captain to demonstrate my resolve. Then, if yours holds, I will have no choice but to kill you and your entire crew."

"If you destroy our ship, you will also destroy your own people."

Does he really think I'm that idiotic? "Your crew requires oxygen to survive, mine does not. I will target your life support systems, located behind the aft nacelle. After every single person aboard your ship suffocates, I will walk over your cold corpses to recover my people." A frigid fury was coursing through him, like nothing he had felt in hundreds of years. He had been completely powerless ever since he was roughly pulled out of that tube and made to carry out Starfleet's dirty work, forcing himself through every repelling task because it was so much better than the alternative. And now he was in control, and he was going to do whatever was necessary to recapture what was his.

"Now…shall we begin?"

Spock glared. Khan repressed a feral grin. He had him right where he wanted him, and Spock knew it.

"Lower shields."

"A wise choice, Mr. Spock." He gave Kirk a vicious kick and calmly walked to the control panel, but inside he was jumping for joy. "I see all 72 torpedoes are still in their tubes. If they are not mine, Commander, I will know it."

"Vulcans do not lie." Evidently their one redeeming quality. Imagine if one learned to – teach it to give false witness, commit the perfect crime. Glad they weren't around in the old days. "The torpedoes are yours."

Khan set the transport coordinates, very determinedly not grinning and crying, and watched as the metallic cylinders were cocooned in light. "Thank you, Mr. Spock."

"I have fulfilled your terms," said the Vulcan. "Now fulfill mine."

"Well, Kirk," Khan mused, "seems apt to return you to your crew. After all – " and one last parting gift from Admiral Marcus rears its head inside his mind as the tiny neurological chip in the base of his skull sends impulses to the forefront of his brain, shoving his consciousness into a tiny screaming corner and he can dimly hear the voice of himself but not himself saying "No ship should go down without her captain!" and feel his hands but not his hands lock the Enterprise within his sights but he can hardly sense anything over his shattered mental screams HE WAS SO CLOSE SO CLOSE

and it was gone. He killed them. He didn't want to.

The chip hadn't done that before. As far as he had known, it was a simple tracking device. It had been one of their first demands. Let us insert this chip into you, or your friends are blown into a million pieces. What could he do but accept?

What's happening?

The Enterprise was in flames. Did I do that? I must have. Oh no, what can I do now? What –

BOOOM!

The Vengeance shook with the force of a devastating explosion. Khan pitched forward out of the chair, falling roughly onto the control panel. How – there was only one way to produce a blast that large, only one source of significant explosives on this ship –

"NNNOOOOOOOOO!"

His life was pointless. He had failed. He. Had. FAILED. He was alone. So completely alone. Fear and pain and flashbacks, before the ship and the cold and the happy and laughing and together back to the days of endless desolation and boredom and self-destruction that he could not ever go through again because he was without anyone and he could simply not do that.

And fury. Rage and fury. (Same thing, idiot.) (Does it matter?) No. He needed revenge. And if the cost of this revenge was his life…

…Good. He couldn't live anymore.

"Set destination," he roared to the ship, voice raw, "Starfleet Headquarters!"

"Engines compromised. Cannot guarantee destination. Confirm order?"

Does it matter? It doesn't matter. Nothing matters. Nothing at all.

"Confirm," he snarled, breathing hard.

The cockpit shuddered and rocked as Khan held on with all his strength, wondering when he was going to die. He hoped sooner rather than later. The ship jolted as it skidded into San Francisco, demolishing buildings and anything that got in its way. Sparks flew and the room began to crumble. The ship tilted a full ninety degrees before coming to a shaky stop.

Khan extricated himself from under the table and slid down the floor to land on the glass window. He swayed unsteadily, trying very hard not to be reminded of another significant encounter with such a height, braced himself, and leaped.

Charging through the crowd, Khan wasn't even sure where he was going, but something in him reminded him of the necessity of disguising himself. He grabbed a long coat, instructed by the same small voice, and pulled it on in a familiar way. He missed his old black one. The one with the collar.

Khan heard a noise, and, turning around, spied a familiar glowing vortex as someone beamed down. Who –

Oh. It was Spock. Not dead?

He started to chase him. Run!

Into a building, through a window, across a street, oddly persistent. Why so persistent? That's not normal; he's got a reason – ah. Someone's died. Someone close to him. Sentiment.

Khan scowled, his face contorting jaggedly. Look where sentiment's gotten me.

Just ahead, a barge was preparing for liftoff. Khan increased his pace, shoving aside the man who attempted to stop him. He won't follow me up there. Too dangerous. He took a flying leap and landed heavily on the barge's roof, only to lose balance again as a new weight on the bottom caused it to shift again. Interesting. That narrows down the casualty to either his girlfriend or his captain.

Spock struggled to mount the roof as Khan strode over and began kicking his fingers, the gun clattering away into space but the Vulcan pulling himself up anyway. He latched onto Khan's shoulder, squeezing the sensitive bundle of nerves, and Khan screamed as pain rocketed through his neck and back. Fighting back dancing black spots, he wrenched Spock's arm away and punched him hard in the face.

After that Khan's brain went on what he called automatic defense mode, fighting without really thinking. There was head-crushing and jumping onto another barge and punching and throwing and kicking and he had Spock's head in his hands and was hearing productive cracking sounds when someone beamed down behind him.

He whirled around at the noise – girl, redshirt, captain's dead then – before she shot him one, two, three, seven times. Impressive – he barely had time to think before Spock grabbed him from behind and hit him hard in the face, wrenching his arm over his shoulder. He screamed as it fractured and Spock threw him roughly to the ground.

The Vulcan knelt over him, punching him again and again, his face slamming against the cold metal of the barge's roof, this is where I die, he's going to kill me, the sentimental idiot killed by the other sentimental idiot, don't you see Vulcan this is what happens when you dabble in emotions – he could feel himself beginning to black out as starburst after starburst of pain exploded across his face – the redshirt girl was yelling something – and then suddenly Spock stopped.

He stared at the girl, incredulous, and then down at Khan. Khan stared back, barely conscious. Why don't you just kill me? Kill me now…Why?

Spock pulled him up slowly by the front of his shirt and cracked him hard across the face. Everything went black.

When Khan floated back into awareness he was lying on a hospital bed, thick straps around his wrists and ankles. His feet were bare. For some reason this gave him a great feeling of vulnerability.

He tried to lift his head to view his surroundings but gasped as a sharp pain ricocheted up the back of his neck. I don't believe I've sustained any major neck injuries, except the nerve pinch and that felt different. Why would they tamper with that area? Neck-down paralysis, as a punishment or to make me easier to handle? Then why restrain me? The only logical explanation is – something to do with that chip? But this of course raised emotions, which he did his best to push down.

Khan heard footsteps approaching – not a guard, too irregular, not particularly businesslike either so someone in the vicinity for a different reason than to come trouble me, a doctor most likely – and a head poked into his limited field of vision. Middle-aged, blue-shirted man. He was correct. "See you're awake, then."

"So it would seem," Khan murmured mildly.

"Well, Khan," the doctor sighed, seating himself in an empty bedside chair, "I really don't know what to make of you. You're a murderous psychopath who's killed hundreds of people, but you are also the reason our captain now has a pulse."

Khan chose not to respond to that. "If you would be so kind as to inform me of what your doctors have done to the back of my neck."

"Tracking device. We had it removed. The boys in Engineering are analyzing it as we speak."

What a bittersweet freedom.

"And what, precisely, are you planning on doing with me? Are you just going to kill me once your precious captain wakes up, when I am of no more use to you?"

"That may be how you treat your prisoners, but fortunately our acting captain has more morals than that. You'll be returned to cryosleep."

Cryosleep. He considers it an act of mercy, of morality, to restore me to that frigid, isolated prison? To be doomed to wake up in some other unfamiliar time, hated and feared and so completely alone? To be woken again and again and forced to do horrible things, my reputation swelling whilst the shadowy figures promising torture and punishment if I renege on my mission grow so anonymously powerful they control everything and anything? To be viewed as the villain in the eyes of humanity every single time, burdened with the knowledge that the only ones who could ever see past this monstrousness died horribly days, years, centuries, millennia ago, until each star supernovas into a sucking black hole and every sun goes dark in the sky? He considers this to be kind? More preferable than death? Khan closed his eyes. He would not cry, he would not cry, he would not – damn.

He struggled to control his breathing as tears dripped down his face. One shaky breath in – stop trembling – and exhale. Again. He could feel the doctor staring awkwardly. "You know, I feel I should inform you – "

Suddenly, a video image popped up on a screen in the wall, showing a rather excited redshirted man holding a tiny, complex piece of circuitry. He spoke with a strong Scottish accent. "Doctor McCoy, ye willnae believe whit we've foond inside 'at bugger Khan's tracker chip – look at this!" He brandished the miniscule device. "It's some sort ay neurological control interface!"

"Neurological – what does that mean, Scotty, speak English!"

"Weel, it could mean 'at he was ne'er actin' ay his own free will - th' Admiral was brainwashin' heem all along!"

The doctor's head swiveled around to look at Khan. "Is this – why didn't you tell us?"

"He was bein' controlled, wasn't he?"

Khan couldn't hear them after this, the world faded to a dull, distant buzzing around him. He stared, fixated, at the screen, or more specifically what was in the room behind the Scot.

"Why," he managed to croak, "why do you have seventy-two cryopods scattered around your engineering department?"

The doctor and the engineer fell silent. For a long moment, no one spoke.

"Tell me," demanded Khan, his voice quiet and dangerous. "Tell me NOW!"

"It's your crew. They're alive," said Doctor McCoy quickly. "Your crew's alive. Spock transported the torpedoes only onto the Vengeance. He left the pods here."

"Let me go." Khan started thrashing against his restraints, ignoring the stabbing pain in his neck. "Please! Let me get down there! I need to get down there! Please!"

"Is what Scotty said true? Was the Admiral controlling you with this chip?"

"Yes! Yes! I didn't want to do it! I didn't want to do any of it!" Not a lie. "Now let me go!"

It was so hard to sit still while the doctor undid the straps, but as soon as they were off Khan leaped out of the bed. He stumbled, fighting off a wave of nausea and dizziness as his neck throbbed agonizingly, but recovered and took off running through the ship. Thanks to a momentary glimpse of the Enterprise's layout while negotiating on the Vengeance, he knew exactly where to go and how to get there – left, straight, right, third door, up the stairs, careful here, left again, right – shoving people out of the way as he flew towards the 72 precious metal pods, their inhabitants sleeping for far too long. He was dimly aware of the doctor and a few guards chasing him, but he outraced them easily.

Here we are – finally – Khan burst through the door, head and heart pounding, staggering slightly but fighting down the pain. There they were. The things he'd fought so hard to protect. The first one that mattered, who had always mattered, was straight at the end. Number 68.

Bare feet slamming on the cold floor, followed by quite a procession of equally confused guards, doctors and engineers, Khan counted down the rapidly passing tubes. 12, 13, 14 – 30, 31 – 54, 55 – 67, here we are, 68. He began the unlocking process, fingers flying expertly over the aged controls. Unlike the current crew of this ship, he had been alive when these pods were designed – in fact, he had helped design them. It was simple child's play to shut off the freezing mechanism and bring the short man with sandy-blond hair back into consciousness.

The machine hissed as the ice receded from the man's face and the door opened. He coughed several times before blinking groggily awake. "Wh…Shr'lck?"

"It's me." Sherlock pulled John into his arms, burying his head in John's shoulder and breathing in that perfect, familiar scent he had missed for so long. He rubbed his hands up and down the man's back, banishing the lingering cold. The dread persona of Khan Noonien Singh flowed away like the tears now freely flowing down his face. "It's me, John. I missed you so much." His voice broke.

The motley assortment of guards, engineers and doctors skidded to a halt at the sight of unfeeling, villainous Khan sobbing brokenly into the shoulder of a man still encrusted with frost. Scotty and Doctor McCoy took this opportunity to explain that they had been wrong about the Augment all along, none of it was his fault and he was quite blameless. This half-truth would propagate around the ship and eventually the galaxy. Nobody needed to know.

"Sherlock…" John gently prised the genius's head from his shoulder, taking his face in both hands and stroking his sharp cheekbones. "You've lost weight. What's happened to your hair?"

Instead of a reply, Sherlock leaned forward and captured the doctor's mouth in a kiss that was infinitely tender and passionate at the same time, attempting to convey the depths of his loneliness and despair and eventual joy at finding and holding him again.

"I love you," he whispered into John's lips, over and over. "I love you, I love you, I love you."

"Sherlock. I love you too."

Sherlock broke away with a half-sob, half-laugh. "I have waited for hundreds of years to hear you say that."

"I'll say it more, then. I love you. I have always loved you, and I will love you for eternity and back, until every sun supernovas and the universe is no more, I will be in love with you, Sherlock Holmes-Watson."

Sherlock shuddered with pleasure and kissed him again. "And I you, John Holmes-Watson."

Finally John pulled away. "The decoys. Everybody's safe?"

"Seventy-two cryopods, right here in this room."

"Oh, thank God!" he breathed. "Here, help me out."

Sherlock chose to interpret this as 'pick me up because I'm still woozy and we haven't really touched in centuries,' so he lifted John out of the pod, giving him a quick hug before setting him down gently. John squeaked with surprise but held on to him. Grinning, Sherlock pressed a soft kiss to John's forehead.

"Khan! What is the meaning of this?" demanded Spock, bursting through the doors and striding into the room. Sherlock tightened his hold protectively on John. He'd be the acting captain, then, predictably. His mind hearkened back to the doctor's statement about his "having more morals" than Sherlock (Khan, at that point.) A Vulcan with morals, how interesting.

"Why is he not imprisoned or asleep? Who was it that released him from the infirmary?" For a species known for being emotionless, Mr. Spock seemed rather incensed. McCoy and Scotty quickly attempted to pacify him with explanations.

John looked up at Sherlock, confused. "What's wrong? Were you being held prisoner? Did you get hurt?"

The other man rested his cheek on top of John's head, tiredly. "People were threatening you, again. Let's talk about this later. I've done some things I didn't want to do."

"Alright. I understand." John brought his hand up to stroke the contours of Sherlock's face.

"Please do."

Spock broke away from the gaggle of well-meaning (well-meaning? When was the last time I've thought the word well-meaning? John must be rubbing off on me already) idiots, coming to a halt in front of the two. "Khan."

Sherlock fixed him with a lethal glare over the top of John's head. "Sherlock Holmes-Watson, thank you."

"Be nice, love," John admonished from below.

"I refuse."

"I apologize for him," said John, sticking out his hand in a gesture of goodwill. The Vulcan looked taken aback, but gingerly accepted the proffered handshake. "John Holmes-Watson. Pleasure to meet you."

"Acting captain Spock. If what Doctor McCoy said was true, please forgive me for my actions. I was under the impression you were acting of your own will."

"…Sherlock, what happened?"

"I said we'll talk later!" Sherlock cried, and buried his face in John's hair.

"Also, I feel compelled to inform you that three of the cryopods experienced some sort of malfunction. Flight records say they lacked enough weight to ever be full, and they show signs of being tampered with recently."

Sherlock's head snapped up with new panic and dread, sending a searing pain down his neck. "Three? Which three?!" He had become tense and stiff, every muscle tremoring slightly against John. "Tell me which three are empty!"

"I believe it was numbers 18, 34 and 56."

The blood drained out of Sherlock's already pale face. "Oh no. Oh no, oh no." He ripped away from John and pounded frantically across the room to the other pods, checking each one desperately for a face. "No," he murmured with each empty one, frenetic mumblings culminating into a scream. "No, no, NO!"

"SHERLOCK!" John shouted, still leaning weakly on his original pod. "What's wrong? Who's missing?!"

The genius looked up, panting raggedly, an expression of terrified, heartbroken horror on his face.

"Hamish, Valentine, and Ender. They're gone."