School for Scheming

When a school is used as the cover for an elaborate plot-centric scheme, usually by a Big Bad or Mad Scientist. This is popular in horror or science fiction, where the story will centre on aliens, witchcraft or other supernatural activity secretly taking place at the school. Often involves brainwashing or forced servitude of the students, or illicit scientific testing being conducted on the students. Spoilers follow, as the True Purpose of the schools is often not known until The Reveal.

The benevolent (mostly) version of this is an Extranormal Institute. Different from Boarding School of Horrors, because it's not a question of the facilities being bad or the teachers or other students being mean—usually everything is outwardly quite nice, because it makes a better contrast with the Terrible Lurking Secret.

Examples of School for Scheming include:

Anime and Manga

Variant: In Death Note, Wammy's Orphanage for genius children really exists in order to find a successor to L.
- Monster does the opposite: the Kinderheim 511 orphanage really exists in order to create a heartless monster to become the next Hitler. They're almost all killed when they find a kid who is exactly what they want and he leaves pretty much everyone dead.
Yu-Gi-Oh! GX. Duel Academia is basically a giant roach motel for Cosmic Horrors, training kids to fight said horrors in the process.
Mugen Gakuen (Infinity College) in Sailor Moon S acts as a front for activities of the Death Busters, aliens from Tau Ceti who possess human bodies and seek to summon Master Pharaoh 90 to end the world.
Neon Genesis Evangelion reveals us during the later parts of the series that every single person in Shinji's class is a pilot candidate. It does make sense to collect all of them into one school as said school is located in the same city which the Scary Dogmatic Aliens are attacking and which houses the Humongous Mecha to fight said aliens. It even makes more sense when it's revealed that the Marduk Institute that selects pilots is a front for NERV itself who can quickly forge the necessary papers, thereby calling up new pilots on their discretion. Just watch episode 18: Unit 03 is completed and is about to be shipped to Japan. Cue NERV approaching Touji, using his sister being transferred to a better hospital as leverage.
- Even the Lighter and Softer Angelic Days manga uses this trope, although only six are positively identified (Shinji, Asuka, Rei, Touji, Kensuke and Kaworu) while the rest are said to be incapable of piloting. Knowing the franchise however, that may be a lie to motivate them.
Hatsukanezumi no Jikan, or Hour of the Mice, takes place in a boarding school where the students are being experimented on.
Afterschool Charisma features a school for clones of famous historical figures; there's lots of plotting going on around them, including the clones being implied to be killed if they don't display the talent of their originals. After all, they're disposable; the scientists can always make another one.
Hakoniwa Academy from Medaka Box, is eventually revealed to be the public staging ground for perfecting superhumans and applying their abilities to all humanity. The chairman reflects on this as the fulfillment of the purpose of all schools: to allow their students to better themselves and advance their abilities. Of course, most schools don't implement it in such Nietzchian terms. And the whole forcing the eventual results on their student population and high death toll, which makes the Academy this trope.

Comic Books

Done in one of the Aspen comic books. It's an odd cross between Corporate Assassination and Geisha-like training. Seriously.
The overarching plot of Stars and S.T.R.I.P.E revolves around Courtney's high school being the cover for the base of the Dragon King, a 40s supervillain. This includes a supervillain art teacher, kidnapped students turned into brainwashed ninjas. and Courtney nearly getting her brain transferred into a giant mosquito due to her cheating on an IQ test.

Fan Works

In Red Witch's Galaxy Rangers fanfic, Miss Abercrombie's "Charm School" turns out to be an elite academy for spies and secret agents from Earth's wealthiest and well-placed families.

Film

Kekko Kamen: "Satan's School For Girls". Seriously who would send their daughter to a school with Satan in its name?

Literature

The title character of The Demon Headmaster hypnotises his students as part of his scheme to take over the world.
In the Spy High books, the characters attend a "school" that's really a training centre for young spies.
Battle School and Command School in Ender's Game. Although they're a bit more transparent and honest about their motives than usual.
Humorous example: In Regarding the Fountain, Dry Creek Middle School turns out to have been built on top of the local natural spring that is the source of the town's famous creek as part of a plot by a pair of Corrupt Corporate Executives to control the local water supply. The nefarious scheme is brought to light when the school drinking fountain needs replacing.
Hailsham, the British boarding school where the protagonists grow up Kazuo Ishiguro's novel Never Let Me Go is really an experiment designed to prove that cloned children would grow up to be as intelligent and sensitive as regular people if raised in the right conditions. That wouldn't seem so bad, except the children get cannibalized for organ donations anyway.
Hampden College, the setting of The Secret History, isn't specifically for scheming—but there's enough of it going around all the same. Richard calls his classics lessons "Julian's private university," which certainly fits this trope.
The Gemma Doyle trilogy.
In Animorphs, the Yeerks, mind-controlling aliens that inhabit their hosts, use a Boys & Girls Club type organization named The Sharing to recruit. The Vice-Principal of the protagonists' school is infested, and the janitor's closet is an entryway to the aliens' feeding grounds.
In the Alex Rider series, Alex attends a corrective school for delinquent rich kids. All is normal until the "changed" students turn out to be genocidal clones of the Big Bad about to use their parent's resources for a new apartheid.
H.I.V.E: the Higher Institute for Villainous Education, is a more obvious one: the kids are told from the start that the aim is to produce Villains.
The Prime of Miss Jean Brodie, where a gang of pupils are secretly coached by Miss Brodie for her own purposes.
The Gallagher School for Girls in I'd Tell You I Love You, But Then I'd Have to Kill You and Cross My Heart and Hope to Spy is a training ground for young female spies and the girls are constantly being thrown into life-threatening situations as "tests".
The Silver Crown has a secret school in it, which brain-washes/trains children as assassins, via the Heironymous Machine.
In Lois Duncan's Down a Dark Hall, the exclusive school Blackwood (it's really really exclusive, it only has four students counting the main character) is really for the purpose of collecting kids with ESP so dead writers, artists, composers, scientists, and mathematicians can use them as vehicles to produce all the things they didn't get to when they were alive. This would be all fine and dandy--in fact, Ruth, the most intelligent of the girls, doesn't mind being used to write down mathematical theories--except that not only can people like Emily Bronte and Vermeer get through, but so can anyone else. Sandy ends up transcribing a terribly vulgar poem in French, and let's not even get into what Lynda paints. Also, Blackwood is not the first school Madame Duret opened; there was one in France and one in England. Of all the students at those schools, four killed themselves and the rest are mental hospitals. And Madame Durect keeps trying anyway.
In The Grounding of Group 6 by Julian F. Thompson, five kids are sent to what appears to be an exclusive boarding school but is really a cover to have them taken into the woods with a hitman hired by the kids' parents to kill them all.
The Learning Institute for the Very Enlightened in The Mysterious Benedict Society, which due to some Fun with Acronyms and Sdrawkcab Name becomes E.V.I.L. The main base of Mr. Curtain (in the first book, anyway) and therefore of all his schemes.

Live Action TV

The new series of Doctor Who plays with this trope. In the episode "School Reunion", the school is secretly run by Krillitanes, who use the children to crack the "Skasis Paradigm", which gives total control of time and space. In "The Sontaran Stratagem"/"The Poison Sky", Luke Rattigan runs a school for gifted teens, planning to repopulate a new world with geniuses after a Sontaran takeover of Earth.
The Sarah Jane Adventures: "Revenge of the Slitheen" has a plethora of schools worldwide being used, via new technology blocks, by the Slitheen in a revenge plot against humankind. They are attempting to use the technology in secret rooms hidden in each of these new buildings to switch off the sun.
Are You Afraid of the Dark? had an episode where two kids discover that their boarding school is run by monsters, who brainwash the students into taking care of alien eggs.
An episode of the new The Outer Limits involved a school where children of wealthy parents are brainwashed and controlled to create political weapons.
The Academy that River was sent to in Firefly, supposedly a school for the exceptionally gifted, but in reality a twisted government/corporate facility where she and others like her were subjected to horrific experiments and brainwashing in order to turn them into weapons.
In Kamen Rider Fourze, Amanogawa High was ostensibly set up to encourage creativity in bright students and lead them towards an interest in space exploration. It's really a front for unleashing the power of the Horoscopes and using the kids for experiments with Switches.
In M.I. High, secret agency M.I.9 maintains a secret base under St. Hope's and employs three students as its top agents.

Tabletop Games

In Maladomini, one of the layers of The Nine Hells of Baator in 3.5e Dungeons & Dragons, there's a school for devils and other lawful evil beings seeking to become corrupters, complete with a training course doing mockups of Material Plane events.

Video Games

In Deus Ex Invisible War, the Tarsus Academies where the player character begins are an arguably more benevolent example, but with a twist: training corporate spies and assassins is their cover story, but they are later revealed to be a front for a corporation called ApostleCorp to develop biomodification technology that will allow them to revive their leaders from stasis and bring about their utopian vision of a "Perfect Democracy". You can choose to side with them in one of the Multiple Endings.
In F.E.A.R. 2 Project Origin, Wade Elementary is actually a cover to test drugs on the children in order to increase their psychic potential.
Disgaea 3 is pretty much this.
Leafmore High School in Obs Cure, which was founded as a way for Principal Friedman to get test subjects for his medical experiments.

Web Comics

The psychic academy in the webcomic Zap
While the titular Gunnerkrigg Court is still simply a morally ambiguous Extranormal Institute, as more is revealed about Jeanne and the founders it seems to be going in this direction.

Western Animation

Subverted in Clone High: The military wants to utilize the clones' inherent greatness to lead the Army, while Principal Scudworth wants them to be the main attraction for his theme park (Cloney Island, natch). Neither of these intentions seems to trickle down to the student populace.
Variation: In Recess The Movie, the school is only used for a secret plot during summer vacation when no one is around. A mad scientist uses it to hide a tractor beam with which he plans to move the Moon in order to send North America into a state of perpetual winter. To improve the students' test scores. And thus be elected President. Or something.
- He was trying to abolish summer break.
In the American Dragon: Jake Long episode "A Befuddled Mind", Eli Pandarus fronted an academy for gifted children in the hopes that one of them could solve a magical puzzle box containing powerful magic.
The episode of Teen Titans that introduced Brother Blood to the series had Cyborg going undercover at the HIVE Academy (no relation to the one in the Literature section) as a villain-in-training named Stone. It's really not all that different from a regular high school (there's a Sadie Hawkins dance, regular lunchroom, etc). The only thing different is the subject matter. The HIVE and Brother Blood exist in comics, but the Church of Blood and the HIVE are totally separate organizations, and neither spent a great deal of time grooming new supervillains in a full on "Xavier School, but evil!" setting. By the way, HIVE stands for Hierarchy of International Vengeance and Extermination.