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It's Been Far Too Long

Summary:

Sherlock Holmes is dead. In his place is Khan Noonien Singh.
After the Fall, Sherlock agreed to undergo the numerous operations required to turn oneself into something more. He took control of the 80 others who also underwent the operation and began taking over the world, convinced that he could do a better job of running it than anyone else.
By the time that Khan controlled half the world, there was only one thing that could have convinced him to leave. A certain army doctor by the name of John Watson.
~
John Watson has been completely focused on survival since his best friend died. One day, three years after Sherlock's death, a familiar black car pulls up next to John. After yelling at the car and attempting to stare down a police blockade, John gets in and is promptly sedated by the syringe wielding Anthea.
Khan Noonien Singh has agreed to take his crew and leave the planet in return for one thing. John Hamish Watson.

Notes:

I have been trying to write this crossover for a few weeks now, and I finally managed it this morning at 2 am. Please forgive any errors and enjoy! :D

(See the end of the work for other works inspired by this one.)

Chapter 1: Operation

Chapter Text

It had been three years. John still couldn't walk past that place without seeing red all over the sidewalk.

Mycroft stopped trying to meet with him after the first year, when all John wanted to do was die, and only the constant, watchful eyes that Mycroft placed in his apartment stopped him from succeeding. “I promise you, there is a reason. You must be patient though.” he would say, just before he handed John another bottle of the drugs that dulled his wits and kept the beautiful-painful dreams away.

John never took them. He paid the price in lost sleep and pain and memories, so bright and strong that it hurt just to breath, but it was worth it a hundred times over, just to see him again, pretending for the barest moment that he could catch Sherlock, and they would go home and everything would be okay again.

John was never able to wake up before the end.

~~~

A black car pulled up next to John, driving slowly next to him as he hobbled down the street, leaning on his cane now more than he ever had, doing his very nest to ignore the car and the man inside it.

Eventually, John heard a soft sigh, the window rolled up, and the car drove away. John tried not to feel too happy.

Two blocks later, the police blocked off the entire street. There were men standing by their cars, and dogs.

“Fine. Fine!” John yelled, glaring at the black car as it slid up next to him, the door opening once again. John dropped down into the car, pulling to door closed behind him, scowling darkly at Mycroft.

“I had no choice.” Mycroft said as they rolled through the barrier, actually seeming a bit..ruffled. “I am terribly sorry for all this. You see, he’ll only bargain for you.” Mycroft said, actually sounding as if he really were sorry.

John had time to think that there was something wrong with this before he felt the needle enter his arm. He immediately twitched away from Anthea, unable to help the betrayed look that was on his face.

“He?” John struggled to ask, already hearing the slight slur in his voice as the drug spread through his system, making it hard to think.

“Who else? My dear little brother.” Mycroft sniffed, watching as John made a strangled sound and passed out, slumped against the seat of the car, his breathing slow and even. Only the small crease between his eyebrows betrayed the beginnings of what John Watson was feeling.

“To the hospital Anthea. Mr. Watson had an operation today.” he said, regretting that this small, broken man had been dragged into the battlefield once again, even as he took a photo, saving it for later, when Watson was ready.

“Yes Mr. Holmes.” Anthea said smoothly, already confirming the arrangements with a few precise clicks on the keys of her blackberry.

~~~

John never wakes up. Anthea organizes his operations, placing them one after the other, with barely any time to recover in between. John Watson will have more than enough time to heal his body while he is in stasis.

As the third shift of doctors filed out, leaving the nurses to clean up, Mycroft flipped open his phone, sending the photo that he had taken at the beginning of all this, adding a short message.

Come and get him.
-MH

The reply is almost instantaneous.

Where?
-KNS

Mycroft thought for a moment before he answered, deciding to choose a place that would remind his brother of the life that he had left behind.

221B Baker Street. 3:00 tomorrow.
-MH

Mycroft looked down at the man before him, looking even smaller than usual as he lay on the operating table. He took one more photo, zooming in on John’s slack face before he walked away.
There were many things that needed to be ready before tomorrow afternoon.

~~~

John went straight from the hospital to the stasis capsule, never even waking up from his sedation. Mycroft tucked a picture into his jacket pocket just before the capsule was sealed, remembering the ridiculous hat which Sherlock had been wearing at the time. It was almost enough to make him smile.

At one o’ clock, John was transported to the pick-up location.

At two forty-five, Mycroft walked in, standing in front of the capsule, purposefully blocking the view of John’s face from anyone who came in through the door.

At exactly three o’ clock, Mycroft looked over at the window as his brother burst in, uncaring of the glass that he broke.

Mycroft sighed. “Do you always have to make an entrance?” he asked, looking with disapproval at the glass spread out over the floor.

The man shrugged, stepping over the glass as he walked toward the capsule, a tiny smile appearing for the barest of instants on his face as he looked down at John.

“You changed him.” he said, turning toward Mycroft, the smile vanishing as he looked away from John.

“I said that I would. I keep my promises Sherlock.” Mycroft said smoothly, purposefully using the name that his brother had abandoned after his ‘fall.’

“I have told you many times, it’s Khan now.” Khan said sharply, advancing toward Mycroft, a murderous glower on his face.

“Does that name bring back too many memories? Very well, Khan.” Mycroft said, hiding his snigger beneath an indulgent look. “When do you plan to leave?” he asked, watching Khan carefully as he waited for a reply. This new version of his brother reacted in strange ways to seemingly innocent questions.

‘He always did that,’ Mycroft amended mentally as Khan stalked toward him. ‘Now he just has the physical abilities and the manpower to back up whatever threats he issues.’

“One week from now. I leave it to you to ensure the petty little countries that we are really leaving.” Khan said before he knocked twice on the table, summoning two of his followers, directing them with a glance to take the capsule.

“Goodbye Brother.” Khan said as he followed John’s capsule out the door.

Mycroft stayed in the flat for a long time after..Khan left, mulling over everything that he had said and done while he was here.

A little grin made it’s way onto Mycroft’s face as he remembered Khan’s reaction upon seeing John. Apparently that was one thing that hadn't changed.

Somehow, Mycroft doubted that it ever would.