1) The School is run by a super villain named Nocaute, which is Portuguese for Knock Out. He's a physical Training character who's been featured in a number of different campaigns. Originally in a game set in Miami in the 1980s, he's worked with super villains, such as Fab inc, Doctor Fright and Shock (whom we call Lady Lightning to keep things simple). A master of Gracie Jujitsu, and is known for having more then a few tricks built into his costume. Gained the power of Longevity in game.
Originally a one off throw away sub-boss baddy, a couple of lucky rolls and some polish turned him into a serious returning villain. He's worked with and against the PCs of different games with different GMs. The guy is a ****, who will stop at nothing to achieve his goal. Very mission focused, with a whatever it takes to win concept. No one likes him, but every player in the group respects or at least fears him.
2) The school is located in or around Acapulco Mexico. The elites of the first world governments are aware of it's general existence but not it's exact location. Nocaute owns the local Police and Governments sufficiently to keep them from nosing around and keeps a low profile.
The Fab inc connection explains why spy sats and tech drones haven't found the place, but I need some cover as to why psionics and magic can't sniff it out. I was kind of thinking about Aztec magic or sub-dimensional space as seen in Vampire Kingdoms, but I haven't set anything down. I choose Mexico because it's cheap and Acapulco because I was there in 1992 with Habitat for Humanity, and it was absolutely gorgeous.
3)A North Korean Scientist (or science team) who was working on weaponized super humans recently escaped from NK, and maybe working here. He/she/they might be selling super powers. NK isn't talking about it, and actively spreading disinformation, so no one is sure what's what.
This is actually the core of the story. Back in 1994, Dr. Fright lead an attack on the US Military's super human research center, going after the final chemical treatments. The PCs basically stopped him, but in my original notes, I have a fire starting in a file room which allowed Dr. Fright's crew the in they needed to get in to a secured area. This adventure supposes that Nocaute grabbed a box or two of those 3.5 inch disks after he locked office workers and Marines in the room to force the PCs to split up. I didn't specify at the time, it was just 'file room', but what if part of that file room was about translating physical media into electronic data. And further, what if Nocaute has just been sitting on this data, waiting.
Separate from that, I have penciled in but not revealed that our North Korean scientist is a single person, female, late 20s or early 30s. Highly IQ, but not a hero category. Loves the upgraded resources for her science, and desperately wants access to Nocaute's longevity for herself.
The powers likely to be gain would be three picks off the super soldier table from PU2, Attempt to make invulnerable, Physical Transformation, and enhanced immune system. Always these three powers for regular humans. Minor League super humans might get those three plus something else, up to the maximum allowed for super soldiers.
4) Have an unnamed character who works here, providing lesser gadgets devices and tools. Not one of the genius categories, that kind of stuff comes from Fab Inc, but conventional body armor with costumes, slap gloves that can also deliver electro punches (for punch damage+1d4 electric+2 slap glove+PS), trick knives and boomerangs and the sort, all kinds of grenades (explosive, smoke, sonic or foam) that look like other things, helmet radios built into masks and those kinds of villain fair.
Not to be a genius cat, but rather someone with access to the full suite of mechanical skills.
5) The purpose of the school is to provide organized bad actors with training for their empowered henchmen. Because who gains super powers has been so random, and the baddies had to hire who ever got the powers, this provided some training to street punks who just happened on a lucky break. The school provides training in the hard to come by and restricted skills. Stuff you usually have to roll 'on the job training' for. It provide the skill(s) selected in a much faster format then the 'going back to school' effort does, but does it with a-7% penalty.
Previously I've used this school to explain how low rent thugs and sub-bosses were a cut above the rest. Advanced hand to hand combat was the focus, but it became kind of a back ground thing or any skill or skill set that didn't fit with the characters. A DM short hand if you will. Now I want to feature it.
6) Features. Has to have weapons training, combat training, explosives training, probably a danger room of some sort, and a couple of class rooms on how police organizations work. Needs to be a medical center or facility. And a recovery room and a bar. A morgue and body disposal area seems likely.
Nothing set in stone here, just penciled in ideas. If you have suggestions, I'm all ears.