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Anime & 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 Johan, 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 Starfish 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.
- Fuuka Gakuen in Mai-HiME pretty much exist for the sole purpose of rassembling all the Himes in the same place so to facilitate the advent of the Carnival.
- 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.
- 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.
Films — Live-Action
- The title character of The Demon Headmaster hypnotizes 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".
- Robert C. O'Brien's 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 Duret keeps trying anyway.
- In The Grounding of Group 6 by Julian F. Thompson, five kids are sent to an exclusive boarding school...whose administrators use the school as a cover to have select groups of students 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 Alias becomes E.V.I.L. The main base of Mr. Curtain (in the first book, anyway) and therefore of all his schemes.
- In Hex Hall, the All-Ghouls School is a cover for the Casnoffs' attempts to raise demons.
- In Animas Conquest, Salva Academy seems to be a front for some sort of eugenics campaign - students who graduate at the top are invited to procreate with one another, and an on-campus research facility is manufacturing bizarre drugs that appear to alter the users' DNA (spontaneous hair/eye color change).
- The "Mr Browser" series of children's novels begins with "Mr Browser and the Brain Sharpeners" in which aliens artificially enhance the intelligence of students at a school as part of a plot to Take Over the World.
- The new series of Doctor Who has a few episodes with this. 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 Outer Limits (1995) 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. Luckily, Simon rescued her from it.
- 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, using the kids for experiments with Switches, and eventually gathering all twelve fully-evolved Switches to open up a black hole that'd destroy Japan and allow the Big Bad to meet aliens and transcend humanity in the process.
- In MI High, secret agency M.I.9 maintains a secret base under St. Hope's and employs three students as its top agents.
- Goosebumps has The Perfect School episode. A school where trouble kids are sent, and they always return as perfect kids. It's hinted that brainwashing is taking place, but in fact, the kids are being cloned. The "perfect" clones are sent back home, while the original kids are locked up in the "Nursery".
- In American Horror Story: Coven, Miss Robichaux's Academy for Exceptional Young Ladies is this - originally an exclusive boarding school for girls that was used as a military base during the US Civil War, it was then taken over by the current generation's Supreme (the most powerful witch alive) and the school was used as a cover for the training of young witches.
- An episode of Midsomer Murders revolved around a boarding school which had an exclusive student organization called the Pudding Club which was in fact the recruitment drive for a decades-old antiques smuggling group. The first murder was because a student discovered what was really going on and chose to leave and was killed in case he went public.
- 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 ObsCure was founded as a way for Principal Herbert Friedman to get test subjects for his medical experiments. After an attempt to discover the secret of immortality went horribly wrong and turned his brother Leonard into a plant monster, Herbert founded Leafmore High as a cover for his experiments and to have a steady stream of test subjects, hoping to find a way to save Leonard.
- The Sith academy in Knights of the Old Republic. The player character can usually use this for their own means. Interestingly, the Light Side path actually requires more dishonesty and subversion than the Dark Side path (as you are forced to rescue people covertly without exposing yourself).
- In ClockUp's Euphoria, this is used during the Lotus-Eater Machine.
- 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: School's Out, 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.
- Cool McCool attempts to track down his six major nemeses (The Owl, the Rattler, Jack In The Box, Professor Madcap and Greta "Green Lips" Ghoul, and Hurricane Harry) who have gathered to form a "College Of Crooks." Their initial assignment is to get rid of McCool.