History Main / EnigmaticInstitute

* The London Arc in ''Anime/TousouchuuGreatMission'' features a whole BossRush of various monsters from Classical Greek mythology and several monstrosities from Victorian era novels appearing one after another, seemingly unrelated aside of their shared theme of [[MonsterMisogyny targeting women]] and a series of riddles heralding their next attacks. After several long and difficult battles, it is revealed that all of those monsters were produced by a secret underground organization lead by a NotSoWellIntentionedExtremist MadScientist.
* ''Manga/TokyoGhoul'': The CCG shows shades of this for most of the Part I of the series, and it becomes a lot more explicit in ''Re:'' where their inner circles become more prominent. Even though their are publicly know to be in charge of suppressing the threat of Ghouls, they also engage in many unethical experiments behind the scenes. [[FromBadToWorse And then Furuta takes over...]]

%%* ''Manga/TokyoGhoul'': The CCG shows shades of this. - '''ZCE'''

In-story, they run the range from heroic to antagonistic. Might be part of a CovertGroup or TheConspiracy. Can also overlap with SafelySecludedScienceCenter, unless the organization's laboratory is HiddenInPlainSight. If commissioned by TheGovernment, this can overlap with NoSuchAgency, for example Area51. More sinister versions often involve a group of [[MadScientist Mad Scientists]].

[[folder:Audioplay]]
* ''AudioPlay/BigFinishDoctorWho'' story "[[Recap/BigFinishDoctorWho076Singularity Singularity]]" features the organization known as the Somnus Foundation: originally a legitimate research group studying sleep disorders, it's inexplicably reformed as [[PathOfInspiration a New Age religion]] offering vulnerable citizens a bright future in return for absolute loyalty. However, Somnus is still performing research behind the scenes, using the money and manpower they gain by running a ScamReligion to fuel experiments into psychic phenomena... and more worryingly, quite a few recruits seem like completely different people after being inducted into the cult. [[spoiler:It turns out that the Foundation became a cult when the lead scientists fell victim to a GrandTheftMe staged by future humans from the NaturalEndOfTime: their experiments are all part of a project to rehouse more of their kind in the bodies of recruits, with the intention of creating a [[DeityOfHumanOrigin psychic singularity powerful enough to change the future]].]]

* ''WesternAnimation/TheSecretOfNimh'': NIMH (which is a real scientific organization) is portrayed in a mysterious but mostly negative light here because the movie focuses on the rats and mice that NIMH experimented on. [[HumansAreCthulhu Not much is shown of the scientists]], but they injected the rodents with a serum that caused them to [[UpliftedAnimal gain human levels of intelligence]]. The rodents escaped NIMH because they were horribly mistreated. Some agents from NIMH later try to track down the rats, prompting them to leave the farm where they had been living to find a new home.

* ''Film/IronMan3'' has A.I.M., Advanced Idea Mechanics. They term themselves a "think tank" and have projects running from renaming War Machine to the Iron Patriot to funding research into creating Extremis super soldiers.

* In the Literature/DoctorWhoNewAdventures novel ''Cat's Cradle: Warhead'', the Butler Institute is secretly researching the transfer of human consciousness into computers, as a way to survive ecological collapse. It gets the occasional ContinuityNod in later books (and even [[Recap/DoctorWhoS30E5ThePoisonSky the TV series]]).

* Creator/StephenKing's novel ''Literature/TheInstitute'' is about a secretive organization in Maine that kidnaps children who are telepathic and/or telekinetic. The children are experimented on by the staff to draw out and enhance their abilities so that [[spoiler:they can be used to assassinate political and military enemies]]. [[spoiler:It turns out that there are Institutes all over the world kidnapping and using children as weapons]].
* In ''[[Literature/TheMagicians The Magician King]]'', the already-secret magical society in which legitimate magicians live and work is revealed to feature a WainscotSociety of safehouses and fight clubs in which Hedge-Witches can work their own illegal magic... and hidden in the most secretive regions of ''this'' underground is the Free Trader Beowulf Group, a covert magical research group buried a SafelySecludedScienceCenter in the south of France. Once Julia Wicker becomes worthy of joining them, it turns out the secrecy is due to them studying the deepest secrets of magic -- some of which have the potential to backfire messily. Their ultimate project is [[spoiler:the summoning of a Goddess.]]

* In ''Literature/TheSchoolForGoodMothers'' mothers who have lost custody of their children due to abuse or neglect must complete successfully a program to learn good mothering skills at the "school", which has more in common with a reeducation camp. The mothers are required to sign confidentiality agreements and if they violate it, they will be entered on a registry for abusive parents that will follow them forever.
* ''Literature/{{Worm}}'' has Cauldron, an institution with access to a secret formula to give people superpowers, which they sell for exorbitant prices to people regardless of whether they want to use it for good or evil, but which they justify by saying having even villains with powers is necessary for when they all team up against [[EvilVersusOblivion the Endbringers' attempts to slowly destroy humanity]]. They stay secret, with their headquarters unknown and in an alternate dimension that one of their capes is capable of providing access to. It later turns out they are also [[spoiler: experimenting on people they kidnap from alternate universes with new versions of the formula which often horribly mess with their bodies]], and are planning this all out to [[spoiler: mitigate the effect of [[TheEndOfTheWorldAsWeKnowIt Scion's upcoming rampage.]]]]

* ''Series/BabylonFive '': The Psi Corps, on the surface, is a kind of combination trade guild and law enforcement agency for telepaths. Behind the scenes, they conduct a variety of research and experiments, usually with the goal of increasing telepathic power or creating new telepaths ([[spoiler:one of which led to what is perhaps the most addictive and dangerous drug in the known galaxy and another which led to the test subject growing so powerful he became [[AscendToAHigherPlaneOfExistence a being of pure energy]]]]), creating cybernetic agents from the recently deceased, and altering minds and personalities ([[spoiler:resulting in the Control personality implanted in Talia Winters and the mental conditioning affecting Mr. Garibaldi for much of the fourth season]]).

* ''Series/{{Firefly}}'': River Tam decided to go to a government-sponsored academy that had a challenging course program that was suited to her extremely high intelligence. Unfortunately, it was a front for some kind of project that resulted in her being experimented on, specifically her brain, in a top-secret lab somewhere. In ''Film/{{Serenity}}'' we actually see some of the labs and it's confirmed that it does have connections to the Alliance government as the lead researcher declares that key members of parliament have observed River, [[spoiler:which allows her to pick what happened to Miranda out of their minds with her new psychic abilities]].
* ''Series/ThePeripheral2022'' has the Research Institute, a powerful organization in 2099 which [[ApocalypseNot brought humanity back from the brink of collapse]] by developing [[{{Nanomachines}} Assemblers]] and "air scrubbers" to restore some stability to the [[GaiasLament ruined world]]. However, the organization, and its leader [[BigBad Dr. Cherise Nuland]] serve as the primary antagonists throughout the first season, given that the protagonist Flynne was [[UnwittingPawn tricked into stealing valuable data from them]] ''and'' because said data includes information about their [[MindControlDevice implants]] and other unscrupulous activities.
* ''Series/ThePretender'': As a child, Jarrod was abducted and raised in a secret organization called "The Centre" where his mentor/instructor, Sydney, puts him through simulations in which he is able to feel what other people would feel and understand the motivations for their actions under the same conditions.
* ''Series/RaisingDion'': BIONA appears to be a prestigious organization that intends on using science to better people's lives, but Dion and Pat eventually realize that animals from Iceland have been captured for studying. The CEO argues that the animals are not being hurt, but it does little to cease the suspicion. Especially when they take Dion away once they found out he has powers.

** The National Intelligence Department (NID) is a civilian oversight organization that is involved in the study of extraterrestrial technology. Their eagerness to acquire said tech brings them into conflict with Stargate Command over and over again. And then the SGC discovers rogue elements from the NID have been actively stealing tech from other worlds. After the corruption has been successfully purged from the organization, the remaining rogue elements go underground, eventually forming another, even more secretive organization simply called the Trust, which continues the NID's earlier activities of obtaining and studying alien tech.

* ''Series/StrangerThings'': Hawkins Labs is located outside of town. The people in the Labs secretly train and study children with telekinetic powers.

[[folder:Podcasts]]
* ''Podcast/WithinTheWires'': The Institute is setting of Season One, and referenced in later seasons, often with people having only heard rumors of it. It is described as having stark white halls and sterile lighting. It also fits the somewhat more sinister version of this as they perform psychological experiments on the patients, make it very, very difficult to leave, and even have a place called the Extensive Studies Lab.
[[/folder]]

* ''Franchise/AssassinsCreed'': Abstergo Industries is a company that has a number of scientific projects to its name, most notably the Animus, which allows subjects to relive events in their ancestors' lives. It is also the current front of the [[KnightTemplar Templars]] from which they make and execute their plans to bring the entire world under their control.

** In ''VideoGame/JetpackJoyride'', Barry infiltrates Legitimate Research, a top-secret laboratory created by Professor Brains as part of his evil plans. The scientists working in it are all clones of his late friend Peter Simpkins, who specialize in creating a variety of {{Improvised Jet Pack}}s and vehicles. On the outside, the lab is disguised as a generic house ([[https://cdn.discordapp.com/attachments/893880683460698172/1039586425013801050/LabFullView.png though rather badly at that]]), and on the inside, it's an EndlessCorridor filled with zappers and missiles.
** ''VideoGame/JetpackJoyride2'' introduces a variety of labs very similar to Legitimate Research in concept, being shady secret organizations controlled by the villains affiliated with Brains. Such laboratories include Subterranean Labyrinth (the lab located inside the mine, and [[NonIndicativeName despite what its name indicates, is a corridor]]), Arctic Industries (located somewhere in the Arctic and partially inspired by the typical Soviet factories), Moon Tomb (heavily based on the Egyptian pyramids), Neontropilis (Japan-influenced but rather dated example of NeonCity) and Catacomb Sewers (resident [[DownTheDrain sewers level]]).
* ''VideoGame/CommandAndConquerRedAlert3'': The ''Uprising'' expansion introduces the corporation [=FutureTech=], the developer of many of the weapons utilized by the Allies during the war. In the Soviet campaign, Dasha and the commander discover they are conducting experiments on human subjects and the story then becomes about uncovering the truth and exposing it to the world.
* ''VideoGame/{{Fallout}}'':
** It was part of the role of the MegaCorp Vault-Tec before the War: they secretly set up the Vaults for different experiments such as human hibernation, epidemiology, or the FEV.
** ''VideoGame/Fallout4'': The Institute is a cabal of scientists and technicians descended from what was once the Commonwealth Institute of Technology. They're primarily known for their creation of Synths, highly-advanced robotic androids barely distinguishable from humans that assault the surface-world for materials and kidnap-victims. The people of the Commonwealth live in constant fear of being replaced by robotic duplicates and are in the grip of paranoia at almost all times. Overseen by the enigmatic "Father," The Institute has fully convinced itself that the surface world is a decaying husk they have every right to pick at while covering their eyes and ears to the moral implications of TheConspiracy they've helped cultivate.
** The ''VideoGame/FalloutNewVegas'' DLC "Old World Blues" introduces a mysterious pre-War group known only as the Think Tank. A privately-owned organization concerned solely with top-secret bleeding-edge research in a wide variety of fields, its existence was only known to a few extremely rich and powerful entities across America, most of whom numbered among the Think Tank's clients. With their underground headquarters hidden under a mountain, their secrecy was maintained so well that they remained undisturbed for over two hundred years after [[WorldWarIII the Great War]]; having [[BrainInAJar achieved immortality of a sort]], they have even been able to continue their increasingly depraved research since then. Needless to say, hilarity ensues when you unexpectedly blunder into their labs.
* ''VideoGame/FinalFantasyVII'': Shinra, Inc.'s Science Department, lorded over by Professor Hojo. Outside the company, it's unclear if the general population even knows of its existence, though they are very familiar with its biggest project, [[SuperSoldier SOLDIER]]. Even within Shinra, only those in the upper echelons of the company have the real picture of what Hojo gets up to. And then, Hojo himself implies a few times that he has an agenda of his own that doesn't necessarily align with his employer's, but he has to at least put on the appearance of working for them since they have the resources that would otherwise be denied to him.
* ''VideoGame/HorizonZeroDawn'': The eponymous Project Zero Dawn is a case where a top-secret project is actually trumpeted and used as a beacon of hope and propaganda, even though no one knows what exactly it's working on. Rumors abound that it is working some kind of super weapon or other means to stop the Faro Swarm, all to keep people fighting in Operation: Enduring Victory, which threw the entire world's population at the robots just to slow them down enough for Zero Dawn to complete its work. In the meantime, Zero Dawn collected scientists from around the world (sometimes forcibly) and brought them to their secure facility where they were given the choice to either join the project or...not. [[spoiler:The AwfulTruth is that Project Zero Dawn is a desperate attempt to restore the earth to life-bearing capability after the Faro Swarm consumes all biological mass. Its true purpose is kept from the public to keep them fighting and to avoid the loss of hope and morale that would come with the knowledge that they are already fighting a lost cause]].

** ''VideoGame/MassEffect1'': Shepard's first encounter with them comes after discovering a squad of marines that had been lured to a thresher maw nest. Later missions reveal that this is not the first time they had done that, one of them being one of Shepard's possible backgrounds as the sole survivor of a thresher attack. There was one other survivor, Corporal Toombs, who was taken by Cerberus and experimented on to study the effects of thresher maw acid. They also were running experiments with Thorian creepers and rachni trying to create expendable shock troops.

*** The game starts with a Cerberus project to bring the deceased Commander Shepard back from the dead, Project Lazarus.

** ''VideoGame/MassEffect3'': Cerberus again has a number of projects, but many of their scientists defect after they begin [[YouHaveOutlivedYourUsefulness to vanish once their projects are complete]]. [[spoiler:Their main project at this point is Sanctuary, set up as a place where people can be safe from the Reaper invasion. Instead, they are taken to be used as test subjects to study how Reaper indoctrination works.]]
* ''VideoGame/{{Portal}}'': Aperture Science is a research company founded by the eccentric Cave Johnson to conduct... scientific research. All kinds of research. Any kind of science, even if seemingly had no practical purpose. While it initially had good success, after an incident involving a prototype technology that eventually led to the portal gun, which resulted in a number of test subjects vanishing, Aperture's fortunes crumbled. Cave Johnson then moved all his more questionable projects deeper into underground labs to avoid further scrutiny.
* ''VideoGame/PokemonSunAndMoon'': The Aether Foundation, which supposedly aims to cure sick/injured Pokémon. However, this is later shown to include [[spoiler:Pokémon that have been frozen to be included in the president, [[FauxAffablyEvil Lusamine's]], collection. She also seeks out [[EldritchAbomination Ultra Beasts]] for the purpose of destroying them as revenge for taking her husband Mohn, which was what the foundation created Type: Null (then known as Type: Full) for.]]

* In ''VideoGame/TheSecretWorld'', it's revealed that during the Cold War, the Soviet government created its own secret society: known as the Red Hand, it was devoted to [[SovietSuperScience researching supernatural phenomena]] and weaponizing them for the betterment of the USSR. Granted authority and resources beyond any normal Soviet institution, the group imbued test subjects with [[LifeEnergy Anima]] and [[OminousObsidianOoze the Filth]] to create "[[HumanoidAbomination Phantom Cosmonauts]]," brainstormed the possibility of using vampires in the space program, tested methods of travelling into [[{{Hell}} the Hell Dimensions]], and even made a pact with the infamous vampire queen Mara to create vampire/human hybrid {{Super Soldiers}}. [[GoneHorriblyRight Most of these programs ended in cataclysmic success]]. Of course, the Red Hand collapsed alongside the Soviet Union, but some of their labs in Romania are still active -- most prominently Facility 10 AKA "[[IDontLikeTheSoundOfThatPlace The Slaughterhouse]]", a self-sufficient laboratory where the super-soldier program continues, though the scientists running the program have all been converted into vampires and all of them are working for Mara by now. The Red Hand is so secretive that even after thirty years spent defunct, the other secret societies are still surprised by the things you can unearth from their bases.

* ''VideoGame/StarCraftII'': At the start of the game, Jim Raynor is approached by his old partner Tychus Findlay who has an offer from the Moebius Foundation, a scientific group studying Xel'Naga artifacts. Their motives are unknown for the most part, but they are paying handsomely for the retrievals, enough to keep Raynor's Raiders going for a while. [[spoiler:It was actually founded by Dominion Crown Prince Valerian, but it's led by Dr. Emil Narud, who turns out to be another identity for Samir Duran, a mysterious figure who assisted the United Earth Directorate in their invasion of the Koprulu Sector, then the Zerg Swarm, then was revealed to be following his own agenda before vanishing. In the aftermath of ''Wings of Liberty'', [[BigBad Amon]] uses Narud to take over the Foundation and use them to start mass creation of his Protoss/Zerg hybrids]].

[[folder:Web Original]]
* The Website/SCPFoundation is an [[TheMenInBlack international secret society]] devoted to capturing and studying all sorts of paranormal anomalies (beings, objects, phenomena), in order to protect the world from supernatural threats and continue preserving a [[{{Masquerade}} façade of "normalcy"]]. Within the Foundation's secret facilities where they contain these SCP anomalies, scientists perform research on [=SCPs=] to better understand how they work and aren't above doing unethical experiments with [[TestedOnHumans human test subjects]] just to record more data. They are willing to do whatever is necessary, including dosing any witnesses they encounter with [[LaserGuidedAmnesia memory-erasing amnestic drugs]], in order to keep all of this supernatural strangeness secret.
* ''WebVideo/KanePixelsTheBackrooms'': The ASYNC Foundation. A secretive government-funded [[ResearchInc commercial research organisation]] which has developed Project [=KV31=], also known as the "Threshold", a device which warps the fabric of reality to open a gateway into [[EldritchLocation the titular Backrooms]]. ASYNC is focused on [[JustThinkOfThePotential commercialising the theoretically infinite space inside the Backrooms]], and they are determined to keep their work secret by [[GasLeakCoverUp any means necessary]], despite the obvious dangers they continue to encounter in the Backrooms.

** ''VideoGame/JetpackJoyride2'' introduces a variety of labs very similar to Legitimate Research in concept, being shady secret organizations controlled by the villains affiliated with Brains. Such laboratories include Subterranean Labyrinth (the lab located inside the mine, and [[NonIndicativeName despite being called a Labyrinth, is a corridor]]), Arctic Industries (located somewhere in the Arctic and partially inspired by the typical Soviet factories), and Moon Tomb (heavily based on the Egyptian pyramids).

* ''WebVideo/KanePixelsTheBackrooms'': The ASYNC Foundation. A secretive government-funded [[ResearchInc commercial research organisation]] which has developed Project [=KV31=], also known as the "Threshold", a device which warps the fabric of reality to open a gateway into [[EldritchLocation the titular Backrooms]]. ASYNC is focused on [[JustThinkOfThePotential commercialising the theoretically infinite space inside the Backrooms]], and they are determined to keep their work secret by [[GasLeakCoverUp any means necessary]], despite the obvious dangers the continue to encounter in the Backrooms.

** The SGC itself, while it is primarily a top-secret military black-ops unit, also has a significant scientific aspect, with several scientists on staff (including [[InsufferableGenius Rodney McKay]]), labs and equipment all suited for studying alien tech. Since the SGC is the focus of the show, they don't seem that enigmatic or sinister to the audience, but those who get a hint of their existence tend to lump them in with all sorts of UsefulNotes/ConspiracyTheories.

*** Another project the game deals heavily with is Project Overlord, an attempt by Cerberus to create a means to control the Geth. [[spoiler:It goes horribly wrong when the project lead, Dr. Archer attempts to use his own brother as the interface, resulting in a rogue AI that kills everyone else and nearly takes over the galaxy.]]

* ''VideoGame/{{Portal}}'': Aperature Science is a research company founded by the eccentric Cave Johnson to conduct...scientific research. All kinds of research. Any kind of science, even if seemingly had no practical purpose. While it initially had good success, after an incident involving a prototype technology that eventually led to the portal gun, which resulted in a number of test subjects vanishing, Aperature's fortunes crumbled. Cave Johnson then moved all his more questionable projects deeper into underground labs to avoid further scrutiny.

** It was part of the role of the MegaCorp Vault-Tec before the War: they secretly set up the Vaults for different experiments such as human hibernation, epidemiology, or the FIV.

[[AC:Anime & Manga]]

[[AC:Audioplay]]

[[AC:Comic Book]]

[[AC:Fan Works]]

[[AC:Film -- Animated]]

[[AC:Films -- Live-Action]]

[[AC:Literature]]

[[AC:Live-Action TV]]

[[AC:Podcasts]]

[[AC:Video Games]]

[[AC:Web Original]]

* ''Literature/{{Worm}}'' has Cauldron, an institution with access to a secret formula to give people superpowers, which they sell for exorbitant prices to people regardless of whether they want to use it for good or evil, but which they justify by saying having even villains with powers is necessary for when they all team up against [[EvilVersusOblivion the Endbringers' attempts to slowly destroy humanity]]. It later turns out they are also [[spoiler: experimenting on people they kidnap from alternate universes with new versions of the formula which often horribly mess with their bodies]], and are planning this all out to [[spoiler: mitigate the effect of [[TheEndOfTheWorldAsWeKnowIt Scion's upcoming rampage.]]]]

* ''Literature/YouFeelItJustBelowTheRibs'': The third part of the book covers the founding of The Institute that was featured in season one of the ''Podcast/WithinTheWires'' podcast. There were two parts of it -- one focused on helping parents forget about the children they'd been forced to give up, and then the more intensive one for those who couldn't be treated by the first.

* ''Podcast/WithinTheWires'': The Institute is the medical prison that the Patient is kept in. It is described as having stark white halls and sterile lighting. It also fits the somewhat more sinister version of this as they perform psychological experiments on the patients, make it very, very difficult to leave, and even have a place called the Extensive Studies Lab.

Scientific research is time-consuming and expensive and usually beyond the means of any one individual. For this reason, scientists typically join organizations that have larger resource pools or the backing of organizations that have deep pockets, corporations, governments or similar. For a variety of reasons, which range from the benign to the insidious, the exact nature of their research might be kept confidential.

In-story they run the range from heroic to antagonistic. Might be part of a CovertGroup or TheConspiracy. Can also overlap with SafelySecludedScienceCenter, unless the organization's laboratory is HiddenInPlainSight. If commissioned by TheGovernment, this can overlap with NoSuchAgency, for example Area51. More sinister versions often involve a group of [[MadScientist Mad Scientists]].

* ''WesternAnimation/TheSecretOfNimh'': NIMH (Which is a real scientific organization) is portrayed in a mysterious, but mostly negative light here because the movie focuses on the rats and mice that NIMH experimented on. [[HumansAreCthulhu Not much is shown of the scientists]], but they injected the rodents with a serum that caused them to [[UpliftedAnimal gain human levels of intelligence]]. The rodents escaped NIMH because they were horribly mistreated. Some agents from NIMH later try to track down the rats, prompting them to leave the farm where they had been living to find a new home.

%%* ''Manga/TokyoGhoul'' - The CCG shows shades of this. - '''ZCE'''

* ''AudioPlay/BigFinishDoctorWho'' story "[[Recap/BigFinishDoctorWho076Singularity Singularity]]" features the organization known as the Somnus Foundation: originally a legitimate research group studying sleep disorders, it's inexplicably reformed as [[PathOfInspiration a New Age religion]] offering vulnerable citizens a bright future in return for absolute loyalty. However, Somnus is still performing research behind the scenes, using the money and manpower they gain by running a ScamReligion to fuel experiments into psychic phenomena... and more worryingly, quite a few recruits seem like completely different people after being inducted into the cult. [[spoiler: It turns out that the Foundation became a cult when the lead scientists fell victim to a GrandTheftMe staged by future humans from the NaturalEndOfTime: their experiments are all part of a project to rehouse more of their kind in the bodies of recruits, with the intention of creating a [[DeityOfHumanOrigin psychic singularity powerful enough to change the future]].]]

[[AC:Film - Animated]]

* In ''[[Literature/TheMagicians The Magician King]]'', the already-secret magical society in which legitimate magicians live and work is revealed to feature a WainscotSociety of safehouses and fight clubs in which Hedge-Witches can work their own illegal magic... and hidden in the most secretive regions of ''this'' underground is the Free Trader Beowulf Group, a covert magical research group buried a SafelySecludedScienceCenter in the south of France. Once Julia Wicker becomes worthy of joining them, it turns out the secrecy is due to them studying the deepest secrets of magic - some of which have the potential to backfire messily. Their ultimate project is [[spoiler: the summoning of a Goddess.]]

* ''Literature/YouFeelItJustBelowTheRibs'': The third part of the book covers the founding of The Institute that was featured in season one of the ''Podcast/WithinTheWires'' podcast. There were two parts of it - one focused on helping parents forget about the children they'd been forced to give up, and then the more intensive one for those who couldn't be treated by the first.

* ''Series/BabylonFive '': The Psi Corps, on the surface, is a kind of combination trade guild and law enforcement agency for telepaths. Behind the scenes, they conduct a variety of research and experiments, usually with the goal of increasing telepathic power or creating new telepaths ([[spoiler: one of which led to what is perhaps the most addictive and dangerous drug in the known galaxy and another which led to the test subject growing so powerful he became [[AscendToAHigherPlaneOfExistence a being of pure energy]]]]), creating cybernetic agents from the recently deceased, and altering minds and personalities ([[spoiler: resulting in the Control personality implanted in Talia Winters and the mental conditioning affecting Mr. Garibaldi for much of the fourth season]]).

* ''Series/{{Firefly}}'': River Tam decided to go to a government-sponsored academy that had a challenging course program that was suited to her extremely high intelligence. Unfortunately, it was a front for some kind of project that resulted in her being experimented on, specifically her brain, in a top-secret lab somewhere. In ''Film/{{Serenity}}'' we actually see some of the labs and it's confirmed that it does have connections to the Alliance government as the lead researcher declares that key members of parliament have observed River, [[spoiler: which allows her to pick what happened to Miranda out of their minds with her new psychic abilities]].

* In ''VideoGame/TheSecretWorld'', it's revealed that during the Cold War, the Soviet government created its own secret society: known as the Red Hand, it was devoted to [[SovietSuperScience researching supernatural phenomena]] and weaponizing them for the betterment of the USSR. Granted authority and resources beyond any normal Soviet institution, the group imbued test subjects with [[LifeEnergy Anima]] and [[OminousObsidianOoze the Filth]] to create "[[HumanoidAbomination Phantom Cosmonauts]]," brainstormed the possibility of using vampires in the space program, tested methods of travelling into [[{{Hell}} the Hell Dimensions]], and even made a pact with the infamous vampire queen Mara to create vampire/human hybrid {{Super Soldiers}}. [[GoneHorriblyRight Most of these programs ended in cataclysmic success]]. Of course, the Red Hand collapsed alongside the Soviet Union, but some of their labs in Romania are still active - most prominently Facility 10 AKA "[[IDontLikeTheSoundOfThatPlace The Slaughterhouse]]", a self-sufficient laboratory where the super-soldier program continues, though the scientists running the program have all been converted into vampires and all of them are working for Mara by now. The Red Hand is so secretive that even after thirty years spent defunct, the other secret societies are still surprised by the things you can unearth from their bases.

* ''VideoGame/StarCraftII'': At the start of the game, Jim Raynor is approached by his old partner Tychus Findlay who has an offer from the Moebius Foundation, a scientific group studying Xel'Naga artifacts. Their motives are unknown for the most part, but they are paying handsomely for the retrievals, enough to keep Raynor's Raiders going for a while. [[spoiler: It was actually founded by Dominion Crown Prince Valerian, but it's led by Dr. Emil Narud, who turns out to be another identity for Samir Duran, a mysterious figure who assisted the United Earth Directorate in their invasion of the Koprulu Sector, then the Zerg Swarm, then was revealed to be following his own agenda before vanishing. In the aftermath of ''Wings of Liberty'', [[BigBad Amon]] uses Narud to take over the Foundation and use them to start mass creation of his Protoss/Zerg hybrids]].

Scientific research is time consuming and expensive and usually beyond the means of any one individual. For this reason scientists typically join organizations that have larger resource pools or the backing of organizations that have deep pockets, corporations, governments or similar. For a variety of reasons, which range from the benign to the insidious, the exact nature of their research might be kept confidential.

The organizations conducting said research obviously tend to be rather tight-lipped about their activities. In some cases, they are outright reclusive. And that's when their existence is even known to the public; in some cases their biggest secret is their own existence. In the cases where they are known, they are often regarded with suspicion by the general populace, because people generally don't like secrets or those who hold them.

* ''Literature/TheRobotsOfDawn'' , Kelden Amadiro, Dr. Fastolfe's chief political rival, creates a Robotics Institute in an attempt to replicate Fastolfe's achievement of RidiculouslyHumanRobots. Not much is shown of its work, but Lije Baley manages to bring Amadiro down by proving that after the Institute failed to deliver results quickly enough, the man tried to speed things along through a GrandTheftPrototype.

* ''Series/{{Firefly}}'': River Tam decided to go to a government sponsored academy that had a challenging course program that was suited to her extremely high intelligence. Unfortunately, it was a front for some kind of project that resulted in her being experimented on, specifically her brain, in a top-secret lab somewhere. In ''Film/{{Serenity}}'' we actually see some of the labs and it's confirmed that it does have connections to the Alliance government as the lead researcher declares that key member of parliament have observed River, [[spoiler: which allows her to pick what happened to Miranda out of their minds with her new psychic abilities]].

* ''Series/StrangerThings'': Hawkins Labs is located outside of town. The people in the Labs secretly trains and study children with telekinetic powers.

** In ''VideoGame/JetpackJoyride'', Barry infiltrates Legitimate Research, a top-secret laboratoty created by Professor Brains as part of his evil plans. The scientists working in it are all clones of his late friend Peter Simpkins, who specialize in creating variety of {{Improvised Jet Pack}}s and vehicles. On the outside, the lab is disguised as a generic house ([[https://cdn.discordapp.com/attachments/893880683460698172/1039586425013801050/LabFullView.png though rather badly at that]]), and on the inside, it's an EndlessCorridor filled with zappers and missiles.
** ''VideoGame/JetpackJoyride2'' introduces a variety of labs very similar to Legitimate Research in concept, being shady secret organizations controlled by the villains affiliated with Brains. Such laboratories include Subterranean Labyrinth (The lab located inside the mine, and [[NonIndicativeName despite being called a Labyrinth, is a corridor]]), Arctic Industries (Located somewhere in Arctic and partially inspired by the typical Soviet factories) and Moon Tomb (Heavily based on the Egyptian pyramids).

** It was part of the role of the MegaCorp Vault-Tec before the War: they secretly set up the Vaults for different experiments such as human hibernation, epidemiology or the FIV.

* ''VideoGame/HorizonZeroDawn'': The eponymous Project Zero Dawn is a case where a top-secret project is actually trumpeted and used as a beacon of hope and propaganda, even though no one knows what exactly it's working on. Rumors abound that it is working some kind of super weapon or other means to stop the Faro Swarm, all to keep people fighting in Operation: Enduring Victory, which threw the entire world's population at the robots just to slow them down enough for Zero Dawn to complete its work. In the meantime, Zero Dawn collected scientists from around the world (sometimes forcibly), and brought them to their secure facility where they were given the choice to either join the project or...not. [[spoiler:The AwfulTruth is that Project Zero Dawn is a desperate attempt to restore the earth to life-bearing capability after the Faro Swarm consumes all biological mass. Its true purpose is kept from the public to keep them fighting and to avoid the loss of hope and morale that would come with the knowledge that they are already fighting a lost cause]].

* The Website/SCPFoundation is an [[TheMenInBlack international secret society]] devoted to capturing and studying all sorts of paranormal anomalies (beings, objects, phenomena), in order to protect the world from supernatural threats and continue preserving a [[{{Masquerade}} façade of "normalcy"]]. Within the Foundation's secret facilities where they contain these SCP anomalies, scientists perform research on [=SCPs=] to better understand how they work, and aren't above doing unethical experiments with [[TestedOnHumans human test subjects]] just to record more data. They are willing to do whatever is necessary, including dosing any witnesses they encounter with [[LaserGuidedAmnesia memory-erasing amnestic drugs]], in order to keep all of this supernatural strangeness secret.

* The Website/SCPFoundation is an [[TheMenInBlack international secret society]] devoted to capturing and studying all sorts of paranormal anomalies (beings, objects, phenomena), in order to protect the world from supernatural threats and continue preserving a [[{{Masquerade}} façade of "normalcy"]]. Within the Foundation's secret facilities where they contain these SCP anomalies, scientists perform research on [=SCPs=] to better understand how they work, and aren't above doing unethical experiments with [[TestedOnHumans human test subjects]] just to record more data. They are willing to do whatever is necessary, including dosing any witnesses they encounter with [[LaserGuidedAmnesia memory-erasing amnestic drugs]], in order to keep all of this supernatural strangeness secret.
* ''Podcast/WithinTheWires'': The Institute is the medical prison that the Patient is kept in. It is described as having stark white halls and sterile lighting. It also fits the somewhat more sinister version of this as they perform psychological experiments on the patients, make it very, very difficult to leave, and even have a place called the Extensive Studies Lab.

** ''VideoGame/JetpackJoyride2'' indroduces a variety of labs very similar to Legitimate Research in concept, being shady secret organizations controled by the villains affiliated with Brains. Such laboratories include Subterranean Labyrinth (The lab located inside the mine, and [[NonIndicativeName despite being called a Labyrinth, is a corridor]]), Arctic Industries (Located somewhere in Arctic and partially inspired by the typical Soviet factories) and Moon Tomb (Heavily based on the Egyptian pyramids).

* ''Podcast/WithinTheWires'' - The Institute is the medical prison that the Patient is kept in. It is described as having stark white halls and sterile lighting. It also fits the somewhat more sinister version of this as they perform psychological experiments on the patients, make it very, very difficult to leave, and even have a place called the Extensive Studies Lab.

Sometimes, it takes a group to make real scientific progress. Sometimes this group decides to work secretly.

Perhaps they don't wish for their comepetitors to get a leg up on them. Perhaps there are those who misunderstand their aims and will try to stop them, regardless of the motivations or results of the research. Or perhaps they're running the kind of experiments that would cause public outcry or invite official scrutiny if they ever came to light. For these and many other reasons, the nature of the science being conducted is kept secret.