Author's note: I've tried to integrate both the Star Trek prime universe and Abrams/alternate universe timelines, though there are some discrepancies. Apologies for any Trek-related problems historically but there's just so much material that I'm sure I've made plenty of errors.
I own nothing, etc. etc.
July, 1981, London
The phone was ringing in Cubicle 1064, ninth floor of the Undershaw Cryogenics Headquarters.
The woman at the desk, visibly recently pregnant, picks up on the second ring without checking the caller number.
"Mary Holmes, hello?" she asks breathlessly. This is the third call she's received in the office today and this time she's hoping that this one will be the one she's been waiting for.
"Hello, Mary." She knows within two syllables from the caller's distinctively resonant baritone who exactly has rang her. Two minutes later, she's cleared her desk and called in with her manager to let him know that she'll not be returning to the office until tomorrow.
It takes Mary six agonizing minutes to reach the lobby of Undershaw HQ, and another twenty or so to find a cab and get back to her flat at the edge of town. By which time she can tell from the voices inside who is home.
She pushes her fare through the cab window and dashes to the door, fumbling for her keys, but her footsteps have been heard and identified just seconds before and the door is opened before Mary can look through her bag. She tumbles into the arms of the tall, dark-skinned and well-muscled man in the threshold, who quickly shuts the door before the cabbie or any onlookers can see them.
"Did the delivery go well?" Khan asks, a couple hours later, in the sitting room. Both the baby and the sitter are out, at Mary's request. Mycroft is at school.
Mary sighs. "No better than the first. I wish you could have been there."
Khan frowns. "I've been busy," he says shortly.
"Will you at least stay around long enough to name him?"
The beige couch creaks when they sit down at the same time. "You haven't even named him yet?" Khan asks, surprised.
She smiles at him. "I was waiting for you. You did so well with the first naming, I though you might as well do the second."
"Mary, I thought we'd agreed that I wouldn't take any part in this one's life. He isn't even supposed to know who I am."
Scooting closer, Mary looks up into his face. "Khan Noonien Singh… You won't even be around to raise him, and if this stupid Botany Bay thing does end up happening he'll probably be long dead by the time you wake up but you might at least have the grace to give our son a name… Unless you want me and the seven-year-old to do it but please, just this once, take some time off your "work" and pick a name?"
"I shouldn't even be in England right now, Mary. I shouldn't be wasting my time on this… triviality. This is becoming a distraction."
"You make that sound like a bad thing," she teases. Sobering up, she adds, "He's your son, for God's sake. I know you can come up with something."
Khan pushes her away. "Mary. I really have to go. I shouldn't have come in the first place, but I thought that I'd check in on you and the baby."
"Any name will do, Khan. Just so long as it comes from you." She isn't pleading, but Mary knows that this may well be the last time she'll see him for a long time. Khan has recently been rather enigmatic on certain topics, been away in Asia far too often, consorting with his fellow Augments. She's afraid that she'll lose him, but they'd both agreed on one thing: this second child will not know who his father is. This is Khan's first visit to London since their child was conceived, and he warns that he'll only be gone longer in the future. Mary will raise the child alone, with the help of their older, seven-year-old son, hopefully.
Khan checks the time. He presses a short kiss to Mary's forehead and stands.
"I love you, Mary," he says, barely audible.
"So you do have a heart." She remains seated and crosses her arms. "I'll be dead, too, by the time you wake up."
Khan crosses to the door and pulls his long coat from the rack. "None of that is certain and you know it. It's a fallback position, nothing more, Mary, and I still don't see why you wouldn't be able to come with me if we did launch the Botany Bay."
"We discussed that, too. I'm neither willing to leave the children nor put them into cryostasis." Mary still doesn't move.
"Then there is nothing else to say on the subject, wouldn't you agree?" Khan pauses with his hand on the door knob.
Mary tilts her head back and looks at Khan out of the edges of her eyes. "Name him? Please, Khan?"
It's his turn to sigh. "I don't know, Mary."
"If you don't, he'll end up being a John or an Andrew or something pedestrian, and you wouldn't like that, would you? Spit it out. I know you've got something." She finally stands.
Khan looks away, begins to turn the handle. Mary runs to him and stops him before the door can open. This time, the kiss is full and when Khan finally breaks it off, they're both more than a bit light-headed.
Before he leaves, he gives her a name.
"Sherlock. Name him Sherlock."
=-o
A decade later, the Eugenics Wars begin and when the entire population of Earth is subjugated by the Augments, Mary is infinitely relieved that she'd agreed to be a single parent to Sherlock.
She had her hands full, regardless. Sherlock can be, regardless of Khan's absence, his father's son, and this both excites and worries Mary. Mycroft is some help, having always been less temperamental. They hope that bringing Sherlock up under the right kind of influence will keep him from going the way of his father, and, most of the time, they appear to be succeeding.
o-=
October, 1991
This time, when Khan comes, he doesn't call ahead and the whole family is home.
Sherlock is the one who answers the door, since Mary is taking a shower and Mycroft is busy with a thin slice of cake, a rare thing these days under the Augment rule, almost as rare as finding one on your doorstep.
Sherlock is ten years old and, of course, he's never seen the man in front of the Holmes flat before in his life, though he seems the tiniest bit familiar. Sherlock, even though he is barely into his double-digit years, doesn't scare easily, but currently, he is frightened out of his trousers. He's heard of the Augments, of course, though most people don't talk openly about them around little children, but he's never seen one before and Khan Noonien Singh terrifies him enough to let the ten-year-old brain know just what is in front of it.
The door closes with a bang that shakes the whole wall and Sherlock runs to find Mummy.
The children, sent out by Mary, are nearly halfway across the city before either adult speaks, and when Sherlock and Mycroft return, Khan is leaving the flat.
Neither of the Holmes children ever manage to discover from Mary what had happened, so what they know is extrapolated from the fact that Mary's left eye and arm are bruised, though she never complains of them. That, plus the stormy expression on the stranger's face as he'd left, and the sad one on Mary's.
That night, for the first time, Sherlock teaches himself what he will later call deleting files from his mental hard drive, but a ten-year-old, even Sherlock Holmes, can only do so much. He is not entirely successful, and dreams of the encounter with the Augment will haunt him for years, though when he wakes up in a cold sweat, he won't know exactly why.
=-o
Another five years pass and the Augment tyrants are overthrown by dissidents among the population, and all are condemned to death as war criminals. Eighty-four are unaccounted for, the notorious Khan Noonien Singh among them, though in an attempt to keep panic levels down, none of the world's major governments, newly reinstated, release this information to the public.
Mary Holmes, one of the foremost firebrands of the uprising, refuses to impart anything to world leaders, on either her part in the rebellion against the Augments or suspicions regarding the missing eighty-four.
All of this is kept quiet and within less than a decade, Mycroft, Mary's first son, is putting the finishing touches on Operation Tabula Rasa.
o-=
Operation Tabula Rasa: the total erasure of the Augment influence, including the destruction or concealment of any artifacts of the era and the distribution of shiploads of propaganda.
By the year 2005, the majority of the public either is convinced that the half-decade under Augment rule was a mass hallucination brought on by an airborne virus, or that nothing had ever been wrong for the last century. The remaining sceptics don't speak up for fear of being thought insane, or do speak up, and are silenced quickly. Mycroft Holmes spearheads the project.
By the year 2006, Operation Tabula Rasa estimates that there are fewer than a half million people on Earth who consciously remember or care what really happened between 1990 and 1996, including several thousand high-up law enforcement agents, a few hundred major politicians, and several world leaders. The rest are mostly either Tabula Rasa enforcers or major figures from the rebellion. And then there are also the strong-minded, those who refuse to forget.
Sherlock Holmes is, unsurprisingly, one of them. Though Mycroft had intended his little brother to be affected by the project, citing his young age during the period as cause, Sherlock refuses to become one of the ignorant masses and Mycroft gives up two years into the project. The animosity remains between the brothers, however, and before Sherlock reaches his majority he has moved out of the Holmes residence and, a few years later, refuses to live in the new, massive estate house that Mycroft has bought for the family.
=-o
The SS Botany Bay — and Sherlock and Mycroft's father — is floating out in space, sub-warp. For almost three centuries, it will be undisturbed.
Meanwhile, Terra spins on and the legacy of the Augments will live on in the world's only consulting detective, though he doesn't know it yet.
Note: My Khan looks like Ricardo Montalbán's Khan. I'll probably be using some lines from Benedict's Khan but the character is mostly based off of Khan Prime. Oh and yes, this Khan is Indian. And he'll be coming back.