The usual Star Trek XI crew, minus Spock, were all on Tarsus IV when Kodos made with the killing, most of them kids at the time, and managed to survive under the radar, with the bridge crew emerging as the leaders because of their age and the fact that they were the ones with the ideas.  Bones is there with his wife and Joanna, but ends up in Kodos's dungeons or otherwise helpless while Jocelyn sacrificed herself to save Jo, who ended up with the kids; eventually he meets up with them, all skin and bones.  Scotty and Keenser are there, too, fresh out of SFA, and when they first meet up with the kids barely trusted at all because the kids have recently learned to distrust authority, and as Starfleet they're authority of a sort.

Most of them go by one name or nickname, especially as time goes on and the younger ones forget their last names and they get more angry at the families that didn't protect them.

A few months in, the other colonists get rescued by Starfleet, who don't realize the kids are there because they're hiding (again, the distrust thing), and it's years before anybody comes back after that--Starfleet again, with Pike.  The kids have survived and done relatively well for themselves, even studying as much or more than they would have if the school for the gifted had still been there, if a bit more unevenly; they have all of the materials, and a lot of them were always motivated to learn, much less now, when a lot of it helps them survive better.

Pike comes in, finds them, and is horrified that they were just left there and wants to get them back to their families...to which they say "hell no".  Eventually he talks them around to a compromise, terms involving at least them leaving Tarsus, and convinces them that the only way anything's going to change is if they change it themselves by finishing their educations and joining Starfleet.  Of course, he thinks they've been on Tarsus for years without education, so it'll be a while before he has to deal with them doing that, since they couldn't possibly pass the admissions tests.

Not so much.  For the next few years, they flood SFA with their admissions, making people look at them funny for only using one name, and for the most part remain together as one big clique on campus.  Well, at least they'll be broken up by their duty positions, Pike thinks.  ...We all know how that went.  They're not in charge of the Enterprise to start with, but JT hooks back up with Scotty and Keenser and takes it over; immediately, the Tarsus cadets snap to higher efficiency and awesomeness than ever before.  Spock is fascinated.

Possibly Tarsus is classified; either way, nobody knows that the kids are survivors unless they were there or have very high clearance.

ETA 04/18/2011--Girl!JT, who is at least as twice as badass as any guy, and BFFs with Uhura except when she isn't. And since Cupcake was totally on Tarsus (how do you think he got the nickname?), the bar scene is totally different. Though, if the plan is to get into Starfleet, I don't know why JT wouldn't be with the cadets. Not too hard to come up with a reason, though; maybe her record's bad enough that the recruiter is all "uh...how about no?", and of course Pike doesn't even look at her record. Hm, maybe not Pike finding them, so there can be the nasty surprise. Or he just didn't remember any of the kids' names, since he didn't know (of) any of them except JT, and didn't meet her, and they all look so different...lol, or he thought JT was a guy at Tarsus, and JT didn't tell him to call her JT in the bar so he didn't have any clue. And JT's crew love her, but Starfleet...not so much. She's got the cult of personality going, and only follows orders when she feels like it, and is a big damn hero, and swears a lot and in general doesn't project the image Starfleet wants to project. But they can't do a damn thing about it.

Bones randomly ambushes the Tarsus people to give them checkups and hyposprays, and they just go along with it because they trust him.

JT learned early on that it was less unsafe to be seen as a boy than a girl; as did the rest of the girls, but JT's better at passing than, say, Uhura. Besides, they all kept their hair short to prevent lice, anyway. JT just never grew hers back or started dressing like a girl after the rescue--she was a tomboy beforehand, anyway. She's not pretending to be male anymore, but with short hair, bone structure that passes for male although she wouldn't look bad as a girl either, a pretty flat chest, and a personality that most people take as masculine, most people don't go around asking. Mostly by accident, she ends up only having sex with people who both are bisexual and for whatever reason don't tell the rest of the Academy that she's a girl. Her first few roommates refused to remain her roommate; eventually the Academy agreed to let her room with Bones because he was the only one who would take her.

The more I think about it, the more this seems like it should end up JT/Uhura. Kicking ass together in the beginning, BFFs for the longest time afterward when they're not fighting, and finally they get together.