Enigmatic Institute

Sometimes, it takes a group to make real scientific progress. Sometimes this group decides to work secretly. For Science!, of course!

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.

Perhaps they don't wish for their competitors 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.

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.

In-story, they run the range from heroic to antagonistic. Might be part of a Covert Group or The Conspiracy. Can also overlap with Safely Secluded Science Center, unless the organization's laboratory is Hidden in Plain Sight. If commissioned by The Government, this can overlap with No Such Agency, for example Area 51. More sinister versions often involve a group of Mad Scientists.

Not to be confused with Extranormal Institute.

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Examples:

Anime & Manga

• Elfen Lied: The Diclonius Research Institute is an organization that studies and experiments on Diclonii and is also running the Lebensborn Project, an effort to replace humanity with Diclonii run by a family who are themselves Diclonii descendants.
• The London Arc in Tousouchuu: The Great Mission features a whole Boss Bonanza 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 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 Not-So-Well-Intentioned Extremist Mad Scientist.
• Tokyo Ghoul: 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 they are publicly admired as the only thing capable suppressing the threat of Ghouls, they also engage in many unethical experiments behind the scenes, and have an entire section dedicated to Tyke Bomb training the children who were left orphaned by the Ghouls. And then Furuta takes over...

Audio Plays

• The Big Finish Doctor Who story "Singularity" features the organization known as the Somnus Foundation: originally a legitimate research group studying sleep disorders, it's inexplicably reformed as 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 Scam Religion to fuel experiments into psychic phenomena... and more worryingly, quite a few recruits seem like completely different people after being inducted into the cult. It turns out that the Foundation became a cult when the lead scientists fell victim to a Grand Theft Me staged by future humans from the Natural End of Time: 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 psychic singularity powerful enough to change the future.

Comic Books

• The Transformers: More than Meets the Eye: Back before the Great War, the Institute was a secret mnemosurgery laboratory where dissidents and other enemies of the state were kidnapped to have their brains tampered with: memory erasure, personality alteration, brainwashing, you name it.

Fan Works

• The Land of What Might-Have-Been:
  • During the backstory, the alternate Elphaba set up a covert research group in order to develop technology for use against the Wizard's government, including such things as the Plague of Transformations and the Slamming Door. Codenamed "The Pottery" and hidden in the sewers of the Emerald City, it recruited scientists and magicians exclusively from the fringes of Ozian society, including a huge number of disenfranchised Animals, with the alternate Boq being hired as an apprentice.
  • In the present-day setting, the Childlike Researchers are a secret society of immortal child prodigies employed by Unbridled Radiance to research new forms of technology and magic for the betterment of the empire. They're so secret that the members are kept hidden away in an underground bunker beneath the Radiant Empress's palace when they're not on official business.

Films — Animated

• The Secret of NIMH: 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. Not much is shown of the scientists, but they injected the rodents with a serum that caused them to 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.

Films — Live-Action

• Interstellar: Since the coming of the Blight, the world has turned away from much of science and engineering research in favor of farming since the current crisis is worldwide food shortages, meaning farmers are what's really needed. NASA was seemingly disbanded (and their accomplishments dismissed as propaganda), but in reality they went underground, literally. A strange anomaly gives Cooper their location at which point their leader, Dr. Brand, gives him the real story: NASA was never shut down, they were just moved off the books so the public wouldn't raise a fuss about it, but they are kept alive because they know life on Earth is doomed so they are running a project to find a habitable world to establish a new home for humanity.
• Iron Man 3 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.

Literature

• In the Doctor Who New Adventures 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 Continuity Nod in later books (and even the TV series).
• The Foundation Trilogy: The eponymous Foundation is established by psychohistorian Hari Seldon to reduce the coming dark age brought about by the imminent fall of The Empire to a single millennium. Initially tasked with the publishing and distribution of the Encyclopedia Galactica, it becomes more and more enigmatic and secretive as time goes on, partially because the neighboring worlds have lost nearly all their technical know-how so the technology the Foundation retains might as well be magic to them.
• The Institute 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 they can be used to assassinate political and military enemies. It turns out that there are Institutes all over the world kidnapping and using children as weapons.
• In The Magician King, the already-secret magical society in which legitimate magicians live and work is revealed to feature a Wainscot Society 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 Safely Secluded Science Center 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 the summoning of a Goddess.
• Most of Monday Begins on Saturday is set in the Soviet "Research Institute of Sorcery and Wizardry", which is not really a secret institution (the way Soviet secret research was), but much rather obscure and lost among the hundreds of diverse research institutes of The '60s. The protagonist has never heard of it at the start of the book and is rather unconvinced to learn that its research goal is "human happiness, like in all of science", but it turns out to be quite accurate.
• The Robots of Dawn: Kelden Amadiro, Dr. Fastolfe's chief political rival, creates a Robotics Institute in an attempt to replicate Fastolfe's achievement of Ridiculously Human Robots. 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 Grand Theft Prototype.
• In The School for Good Mothers, 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.
• You Feel It Just Below the Ribs: The third part of the book covers the founding of The Institute that was the setting of season one of the Within the Wires 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.

Live-Action TV

• Babylon 5: 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 (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 a being of pure energy), creating cybernetic agents from the recently deceased, and altering minds and personalities (resulting in the Control personality implanted in Talia Winters and the mental conditioning affecting Mr. Garibaldi for much of the fourth season).
• Dispatches From Elsewhere: The Jejune Institute, led by the enigmatic Octavio Coleman Esq., appears to be a very strange scientific corporation that works on bizarre inventions such as personal force fields, VR replications of people's memories, and methods of communicating with dolphins. Part of the game the show revolves around is the protagonists trying to determine if Jejune is good, evil, or potentially a front for a data mining scam.
• Doctor Who: The Torchwood Institute is started by Queen Victoria as a defensive organization against aliens and supernatural threats. Over time, it becomes more powerful and more secretive, researching aliens and alien technologies, with special priority given to the Doctor, and investigating strange anomalies. One such anomaly leads to their downfall as it brings about a war between Cybermen and the Daleks. Captain Jack later reforms it, becoming the basis of Torchwood, though it's much smaller and less powerful, but even more secretive.
• 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 Serenity (2005), 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, which allows her to pick what happened to Miranda out of their minds with her new psychic abilities.
• The Peripheral (2022) has the Research Institute, a powerful organization in 2099 which brought humanity back from the brink of collapse by developing Assemblers and "air scrubbers" to restore some stability to the ruined world. However, the organization and its leader Dr. Cherise Nuland serve as the primary antagonists throughout the first season, given that the protagonist Flynne was tricked into stealing valuable data from them and because said data includes information about their implants and other unscrupulous activities.
• The Pretender: As a child, Jarrod was abducted and raised in a secret organization called "The Centre" where his mentor/instructor, Sydney, put him through simulations in which he was able to feel what other people would feel and understand the motivations for their actions under the same conditions.
• Raising Dion: 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 after finding out that he has powers.
• The Secret World of Alex Mack: The Paradise Valley Chemical Plant has been conducting secret research into a new kind of chemical, GC-161 (intended to be some kind of wonder weight control pill), but when things threaten to expose their activities, they go to extraordinary lengths to track down any possible leaks, both to protect their product and because GC-161 contains illegal substances. Their most persistent loose end is the unknown kid who was drenched in the substance when the truck transporting it crashed. They spend the rest of the series trying to identify and secure this kid.
• Stargate SG-1:
  • 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. Then the SGC discovers that 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.
  • 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 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 conspiracy theories.
• Stranger Things: Hawkins Labs is located outside of town. The people in the Labs secretly train and study Psychic Children.

Video Games

• Assassin's Creed: 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 Templars, from which they make and execute their plans to bring the entire world under their control.
• Barry Steakfries:
  • In Jetpack Joyride, 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 Packs and vehicles. On the outside, the lab is disguised as a generic house (though rather badly at that◊), and on the inside, it's an Endless Corridor filled with zappers and missiles.
  • Jetpack Joyride 2 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 a corridor, despite what its name indicates), 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 Neon City) and Catacomb Sewers (resident sewer level).
• Command & Conquer: Red Alert 3: 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 that they are conducting experiments on human subjects and the story then becomes about uncovering the truth and exposing it to the world.
• Fallout:
  • This was part of the role of the MegaCorp Vault-Tec before the Great War: they secretly set up the Vaults for different experiments such as human hibernation, epidemiology, or the FEV.
  • Fallout 4: 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 The Conspiracy they've helped cultivate.
  • The Fallout: New Vegas 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 the War; having achieved immortality of a sort, they have even been able to continue their increasingly depraved research since then.
• Final Fantasy VII: 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, SOLDIER. Even within Shinra, only those in the upper echelons of the company have the real picture of what Hojo gets up to. 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.
• Horizon Zero Dawn: 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 abounded that it was working some kind of superweapon 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. The Awful Truth is that Project Zero Dawn was a desperate attempt to restore the earth to life-bearing capability after the Faro Swarm consumed all biological mass. Its true purpose was 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 were already fighting a lost cause.
• Mass Effect: The secretive organization called Cerberus is a presence throughout the original trilogy. While they have a number of goals they work toward in a variety of theatres, they also have a variety of scientific endeavors.
  • Mass Effect: Shepard's first encounter with them comes after discovering a squad of marines who had been lured to a thresher maw nest. Later missions reveal that this was 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.
  • Mass Effect 2:
    • The game starts with a Cerberus project to bring the deceased Commander Shepard Back from the Dead, Project Lazarus.
    • Another project the game deals heavily with is Project Overlord, an attempt by Cerberus to create a means to control the Geth. 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.
    • A smaller one is Project Firewalker, which is tracking a pair of scientists who were hunting Prothean artifacts.
  • Mass Effect 3: Cerberus again has a number of projects, but many of their scientists defect after they begin to vanish once their projects are complete. 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.
• Portal: Aperture Science is a research company founded by the eccentric Cave Johnson to conduct all kinds of scientific research, 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.
• Pokémon Sun and Moon: The Aether Foundation, which supposedly aims to cure sick/injured Pokémon. However, this is later shown to include Pokémon that have been frozen to be included in the president, Lusamine's, collection. She also seeks out 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.
• Resident Evil: Umbrella Corporation is a big pharmaceutical company in Racoon City. The company secretly makes different types of viruses, particularly the T-Virus and the G-Virus.
• In The Secret World, 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 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 Anima and the Filth to create "Phantom Cosmonauts", brainstormed the possibility of using vampires in the space program, tested methods of travelling into the Hell Dimensions, and even made a pact with the infamous vampire queen Mara to create vampire/human hybrid Super Soldiers. 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, a.k.a. "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.
• Skullgirls: Nine Anti-Skullgirls Labs were created, with only two existing in the present, Lab 8 and Lab 0. Lab 0 is the secretive one that researched Skullgirl blood and have conducted more amoral/immoral research than the other labs.
• StarCraft II: 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. 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, Amon uses Narud to take over the Foundation and use them to start mass creation of his Protoss/Zerg hybrids.

Web Originals

• Kane Pixels' The Backrooms: The ASYNC Foundation is a secretive government-funded 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 the titular Backrooms. ASYNC is focused on commercialising the theoretically infinite space inside the Backrooms, and they are determined to keep their work secret by any means necessary, despite the obvious dangers they continue to encounter in the Backrooms.
• The SCP Foundation is an 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 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 human test subjects just to record more data. They are willing to do whatever is necessary, including dosing any witnesses they encounter with memory-erasing amnestic drugs, in order to keep all of this supernatural strangeness secret.
• Within the Wires: The Institute is the 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.
• 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 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 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 mitigate the effect of Scion's upcoming rampage.

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