I know this story should technically be in the cross over section but thats a much smaller reader pool, so I put it here and also on AO3. If you enjoy please review :)

The chase had taken it's toll on them.

They'd even lost a few along the way and the SS Botany Bay was a little worse for wear. Nothing serious, but certainly more than they were used to. Usually Sherlock reveled in the excitement and puzzle solving that was a good chase, then again, usually he was the one doing the chasing. Seventy five of them had managed to get aboard the ship before he'd been forced to take off, abandoning those few left behind to their fate.

Starfleet had pursued them of course, but Sherlock was too clever for the likes of them and they had escaped. So now here they were, floating behind some moon on the far end of the galaxy. Mycroft had just shut off their systems, leaving them completely invisible to any craft that passed by this quadrant. Not that any would, Sherlock had done the calculations, odds were nobody would find their hiding ship for hundreds of years.

"What do we do now?" Lestrade had asked when they had finally gotten settled, "Just, float through space for the rest of our unnaturally long lives?"

"Cryogenic tubes." Mycroft replied, "Enough for all seventy five of us, we'll wait out here for however long it takes for those traitors to destroy themselves and then we will find ourselves a new home in the future."

It was not a perfect plan but Sherlock had no better ideas.

Currently, seventy three of said cryotubes were activated, their occupants set to sleep for the next few hundred years. Only Sherlock and one other were still awake. Sherlock found him on the deck of the ship, watching the stars.

"It's a long time to be sleeping." John sighed.

"It will not feel so." Sherlock replied.

"I still think we should have stayed, we should have fought." John growled, not meeting Sherlock's eye, "We're smarter, stronger than them, we could have won!"

The control panel began to groan as John's grip began to crush it.

"Human's like to pretend they are God, they meant to create an army of perfect soldiers and they succeeded." Sherlock smirked, "They just didn't count on us thinking for ourselves."

The eugenics program that had seen them and their companions born began almost forty years ago now. At first it was wonderful, then Starfeet began to worry that Sherlock and his kind would rise up against them and decided it was better to strike first than be struck.

"Come, the sooner we sleep the sooner we can wake in a better time." Sherlock called, heading off the bridge and toward the cryorooms.

"Six hundred years..." John mused, stretching before climbing into the cryotube, "I'm going to have some killer bed head."

Sherlock chuckled.

"See you in six centuries." He joked darkly.

"You'll probably be late." John teased, pulling the door closed and initiating the freezing process.

Sherlock followed suit.

His last thought before falling under was to hope that when he woke up, they would indeed find themselves in a better place.

-oOo-

Just as he'd told John he felt as if he'd only just closed his eyes when once again he found them opening. He expected the room to be full of cold fog and several of his companions, John included, stretching out their sore muscle. Instead he saw a group of strangers observing him from inside an unfamiliar white room.

His mind was sluggish from years of disuse but it still took him only moments to deduce hat his cryotube had been moved and he was now under surveillance. Warily he sat up, facing the small group of scientists

"Why am I here?" He asked cooly, "Where is my ship and crew?"

"We have commandeered them." A voice replied, not from the group of scientists but from the other side of the room.

This man was clearly not a scientist, he wore a strange dark suit with a silver pin. Sherlock felt his blood boil as he studied the design, it was different but it was unmistakably Starfleet.

"Out tests show you and your crew age quite well." He continued, Sherlock could practically here John within his mind answering 'we moisturize'. Sarcasm had never been Sherlock's forte, so he kept the silent joke to himself.

"Three hundred years just floating in space, we thought you'd be grateful."

"You should have left us." Sherlock sneered, "Where are they? What have you done with them?"

"They are still safely asleep." The man answered calmly, "If you wish them to stay that way I suggest you co-operate."

-oOo-

Two years.

Two long years had passed since he'd woken. Two years under Admiral Marcus's thumb, building weapons, designing space ships in secret, being called John Harrison. He had to chuckle at the irony of being named John. Marcus, to his knowledge, did not know the name of his crew so it had been coincidence. However, if he had to choose an alias, John wasn't a bad name to go by.

He'd not left Area 31 since he'd arrived here all that time ago. He'd not been allowed to wake any of his companions, nor did he want to make friends with any of the human scum that worked there.

It had been lonely.

The Admiral explained that they had located his ship and his crew some time ago, identified them as the Augment's who'd fled nearly three hundred years ago and decided to put him to use.

Several times he'd considered escape, but he couldn't leave his crew, nor could he find a way to discreetly smuggle all seventy five of them away. He was trapped.

It had taken him a while but he'd located John, still fast asleep of course but his presence gave Sherlock some form of comfort.

"Mycroft would probably laugh at me for engaging in conversation with a frozen person." He sighed, sitting by the tubes, "You'd say it was some sort of coping mechanism, maybe you're right."

John was, for once, stubbornly silent.

"Why is it when I want you to talk you don't reply?" Sherlock sighed, "Before I could never get you to shut up. Still, better company than Anderson."

Finally, he saw an escape.

Marcus wanted torpedos, halfway through the design Sherlock realized they were roughly the same size as a cryotube. It had taken all his stealth and wit to sneak the seventy five members of his crew into the weapons but he'd done it, even managed to load them into a ship ready to flee. But of course, luck was not on his side.

Alarm bells rang and Marcus came for him, he had no choice.

Logically he knew his best chance of rescuing the rest of his strange family was to flee and then attack from the outside. It still filled his heart with guilt to hit the transport button upon the ship and disappear, leaving them all behind.

He spent the next few months planning, learning the history of the past three hundred years he'd slept through. It took time, but soon he was almost ready to attack Area 31 and take back his crew.

But Marcus beat him to it.

He'd felt his heart clench when he saw the news.

"STARFLEET USES NEW PHOTON TORPEDOS TO HOLD OFF ROMULAN ATTACK FORCE AT BETA CENTARI EIGHT."

Marcus had fired the torpedos.

The torpedos he'd made. The ones containing his friends, his family.

Mycroft, John, Molly, Ms. Hudson and so many more, all dead.

He'd promised them a new life and he'd failed, he'd lead them to their death.

John, his first officer, his doctor, his best friend, he'd killed him.

That's when Sherlock decided that Marcus was going to pay, he was going to make sure of it, even if it was the last thing he'd ever do.

Long prologue I know!

IMPORTANT

I'm going to skip forwards now to after Pike was killed and begin when Spock, Jim and Uhura go to Chronos because up until them everything happens as it does in the film and rewriting it is a bit of a waste of time don't you think?

BUT if you guys really want me to I can rewrite the scenes but it will take me a while and everything will happen exactly as it did in the film, there will be no changes.

I finish the term in two weeks, once I finish school updates will be faster but until then they should be every 4-5 days.