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"And I made a website to enhance everyone's lives!"
"We are the Invisible Hand. We are the Illuminati.
We come before and after. We are forever.
And eventually... eventually, we will lead them into the day."
Morgan Everett, Deus Ex

The Conspiracy that secretly rules the world and manipulates the lives of the common muggles is, for a change, actually a force for good rather than evil, though perhaps not lawful, depending on who runs the Government. Indeed, a Benevolent Conspiracy might actually be run by the Government, in order to discreetly fight against evil, or at least to protect the interests of the people they lead. (Which is probably not to say "the current administration"; these kind of secret conspiracies are looking to a longer view.) One such goal of this conspiracy might be to work against a more powerful enemy without provoking an all out fight against them, or to prevent the populace from breaking out in a counter-productive panic by revealing things to them before they are ready.

Despite their intent, a Benevolent Conspiracy can still be antagonists. Well-Intentioned Extremism is a danger for any viewpoint, and there's always the possibility of a Renegade Splinter Faction developing. It's even possible that they just screwed up and designated the protagonists as enemies when they were really on the same side. And regardless of whether they're really the good guys, they probably don't appreciate being revealed and will take steps to prevent it (though the truly good ones will probably just steal the evidence rather than Make It Look Like an Accident).

Contrast the Nebulous Criminal Conspiracy, which is very definitely evil. If run by the government, it's likely a case of No Such Agency. Like a regular conspiracy, may be headed by an Omniscient Council of Vagueness (and, since Good Is Dumb, are much more likely to be a Not-So-Omniscient Council of Bickering than usual). May overlap with an Ancient Order of Protectors, particularly when a Sealed Evil in a Can is involved, though they're more often an Impartial Purpose-Driven Faction.


Examples:

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    Anime and Manga 

    Comic Books 
  • In one two-part Amazing Spider-Man story during Eric Larson's run, Spidey teamed up with The Punisher to find out who was hoarding thousands of tons of cocaine but not selling it. It turned out that an agency in the actual U.S. Government (which one was not revealed) was behind this scheme. Worried that the economy's dependence on the Gold Standard might be a liability if gold were to lose value in a crisis, this agency was actually considering using cocaine as the new standard, reasoning that drugs always had value. While both Spider-Man and the Punisher knew this was a sick and misguided idea, they decided against exposing it; not only would it be hard for a judge to believe "a man in a mask like me and a walking gun shop like you" as Spidey put it, knowing about such a thing would hurt — if not destroy — what trust remained in America's government. (However, they did destroy the cocaine. Letting the conspiracy continue was not an option.)
  • In Paperinik New Adventures, the US government goes out of its way to hide the existence of the Evronians to prevent a nation-wide panic if the public found out there's an Horde of Alien Locusts ready to invade Earth-and the one time federal agent Mary Ann Flagstarr stumbled on Xadhoom she flat-out admitted they're not the only thing the government hides for such reasons (and that's why she's not going to investigate Xadhoom as long as she's not a danger). On his part, Paperinik implicitly agrees on this by keeping the secret even before finding out the government knew, and in a few occasions had to prevent the release or discredit evidence of them.
    • Their point is proven in "Might and Power", when Grrodon's Evronians launch an attack in such a way it cannot be covered up and do cause widespread panic-at least until NATO defeats them.

    Fan Works 
  • In the fanfic Equestria: A History Revealed, amid the insane conspiracy ramblings, the narrator actually uncovers some information hinting at a genuine conspiracy. In chapters 11 and 12, she finds evidence of a secret meeting between Celestia, Luna, and Star Swirl the Bearded — just before Celestia and Luna became alicorns and were crowned Princesses — and all record of what exactly happened at this meeting was erased. The narrator tries to spin this as evidence that Celestia is actually evil, but the documents strongly imply the conspiracy was for the greater good of Equestria, as it prevented the complete collapse of the nation after the defeat of Discord, and restored stability to the nation by creating a central leadership figure for the ponies to believe in.
  • In TRON: Endgame Scenario, the Agents of Ma3a are this. Most know that Administrator Ma3a has a network of Programs across Cyberspace to act as her hands and eyes, as she cannot leave her dock. What isn't know is that Ma3a is actually Lora Baines-Bradley (part of her anyway), who was digitized by her own laser invention and, realizing that there were enough unethical humans who would exploit the Programs, is trying to reform the Program world so that it's closer to an equal partnership with humanity.
  • My Huntsman Academia has the same conspiracy as in RWBY, only Izuku and Toshinori are in on it as well due to being the current and former holders of One For All. Ozpin deliberately keeps Izuku in the dark about the more sensitive matters to let him live out his school life in relative peace for a little while longer, having learned the dangers of putting so much pressure on his subordinates so early in his careers from the dissolution of Team STRQ.
  • This Bites! has the New World Masons, an alliance of pirate crews and a splinter sect of Marines who are working together to enable the latter to overthrow the World Government and end its corruption.

    Film 
  • The Bureau for Paranormal Research and Defense from the Hellboy films (as opposed to the comics, where they worked openly). This is a secret organization that protects the world from supernatural dangers.
  • Men in Black: A secret agency on Earth, which started as a Government Conspiracy (but avoids them now, because "they ask too many questions"), covertly coordinates with alien governments to control alien immigration to and from Earth, as well as carefully controlling the importation of advanced alien technology.
  • The Medjai in The Mummy Trilogy, a secretive organization that actively works to prevent explorers from unearthing Imhotep's tomb, including outright killing innocents in order to keep the secret.
  • The Brotherhood of the Cruciform Sword in Indiana Jones and the Last Crusade were/are a group sworn to keep the Holy Grail a secret and away from those who would misuse its gifts. They have little problem with trying to kill those who would seek the Grail, as they are backed by divine will. Nor do they have a problem with dying themselves to keep it secret if they have to. (MAD, of all things, pointed out in their satire how hypocritical it would be of an organization dedicated to protecting the memory of Jesus Christ to resort to methods he would clearly not approve of.) Indy's response that he just wants to find his father to Kazim's question below shows how benevolent they are, giving him info on how to find him.
    Kazim (To Indy): Ask yourself, why do you seek the Cup of Christ? Is it for His glory, or for yours?
    Indy: I didn't come here for the Cup of Christ. I came to find my father.
    Kazim: In that case, God be with you on your quest. Your father is being held in the Castle of Brunwald on the Austrian-German border.
  • The Dark Universe has Prodigium, a secret organization that protects humanity from evil and studies monsters. It is headed by Dr. Jekyll (Russell Crowe) and first appeared in The Mummy.
  • The Midnight Meat Train: The conspiracy behind Mahogany and his butchering of subway passengers is to ensure that the evil entities living underneath the city are given regular human sacrifices and the rest of the population are kept safe from their hunger.
  • In Monsterverse, Monarch operates as a clandestine government organization dedicated to researching and combating Kaiju (known by the organization as M.U.T.O.s or Titans).
  • Before the beginning of Sausage Party, all food items knew the Awful Truth of what happened to them if they got chosen, so The Non Perishables invented the myth of the Great Beyond to at least Let Them Die Happy.
  • The titular organization of The Adjustment Bureau leans pretty heavily on the "works in mysterious ways" card, is willing to do some rather unscrupulous stuff to ensure their plans come to pass, and have to make some harsh "needs of the many" decisions, but they genuinely do care for the overall well-being of humanity. The movie implies they only intent to guide humanity until humanity is mature enough to have free will, and The Chairman will rewrite His own plan to account for the wills of humans who sufficiently prove themselves to Him.
  • Greenland: The US government begins recruiting people to evacuate as soon as an ice fragment destroys Tampa. This is a subtle clue that the authorities have known for some time just how serious the situation is, and is suppressing the truth to avoid mass hysteria. Considering the crowd of people that breaks through the barriers of the military base, overwhelms the soldiers, and accidentally blows up several of the planes taking refugees away, maintaining silence might have been the correct thing to do.

    Literature 
  • Isaac Asimov
    • "The Dead Past": The government is secretly trying to prevent anyone from developing a time viewer device (a device that can show the past). The protagonists disagree and not only develop such a device, but distribute the plans widely. A government agent then explains to them the reason for the ban: such a time viewer could be used to spy on anyone, anywhere in current time. The widespread availability of such viewers means the effective end of personal privacy for the human race.
    • Foundation Series:
      • The Foundation Trilogy: The Second Foundation is the opposite of the Foundation on Terminus in many ways; established at "the opposite end of the galaxy", a secret cabal of mentalists rather than a public presence of scientists and engineers, but both are present to prevent thirty thousand years of anarchy that would occur without following the Seldon Plan.
      • Foundation and Earth: This novel contains a major reveal; R. Daneel Olivaw, a Three Laws-Compliant robot, has been benevolently guiding humanity's path since Robots and Empire. The prequels also explore this conspiracy, including the way the spoiler character had helped Hari Seldon develop his Seldon Plan.
    • "Mother Earth": The Pacific Project is a three-stage conspiracy by a handful of Earthmen:
      1. Capitalize on the superiority-complex of the Outer Worlds by provoking them to unify against the "inferior" Earthmen.
      2. Provoke the Outer Worlds into a war which they win easily and quickly, causing resentment and desire for revenge within the general population of Earth.
      3. Wait... for a century, even. Each of the colonized worlds are imperfectly terraformed, and will develop unique mutations. Meanwhile, Earth will unite and prepare a Terrestrian Empire that is ready to evolve into a Galactic Empire.
  • In the Belisarius Series, the good guys who are movers and shakers of the Byzantine Empire begin their plans for dealing with the evil Malwa without telling the Emperor or Empress, the former of which being something of a paranoiac who sees conspiracies against him and doesn't really trust the titular general out of fear Belisarius' Cincinnatus behavior is just an act, and not for real. This is a downplayed version as Empress Theodora later joins them.
  • In Dance Of The Butterfly, the wealthy and powerful Felcraft family fully embraces their self-imposed duty of protecting humankind from a threat it doesn't even know exists. Keeping this threat a secret, as well as thwarting it, is part of the cover-up.
  • The NSA is portrayed as one in Digital Fortress.
  • The Dresden Files: The White Council of wizards attempts to be this for humanity, although opinions are strongly divided as to how well it succeeds. In fact, the official party line's denial of the existence of an evil conspiracy in their midst (despite strong evidence) prompts some characters to form a Benevolent Conspiracy of their own, so they can act against the evil one without censure from their higher-ups.
  • The Last Adventure of Constance Verity: There is an expansive number of secret societies and organizations on and off-world who conspired to ensure that Constance would fulfill her destiny to become The Chosen One and keep the universe from collapsing into entropy as Engine Theory dictates. They even conspired every factor in her personal life since the moment she was activated to make sure she had a proper work-life balance, both to maximize the positive results of her adventuring and to keep her from discovering the truth. This is deconstructed when Connie finds out about it, as while everyone else seems to think it was all worth it given all the good she's done, she is not happy to feel manipulated into fulfilling a role she never asked for. Nor is she happy to find out that what little normalcy and stability she ever had was itself just another facet of the constant weirdness she attracts.
  • The Forsynthia Club of The Last Binding are a group of four women who guard the pieces of the Last Contract to keep malicious forces from using them to seize control of Britain. Unfortunately, someone is tracking them down and murdering them one by one. In A Restless Truth, it's revealed that this is because one of their number, Sera Hope, turned traitor when Flora refused to use the Contract to gain power, and has been working with the Coopers to track them down.
  • The Order of Solomon in L. Jagi Lamplighter's Prospero's Daughter. Utterly ruthless about quenching all knowledge of the existence of magic — so people resort to trying to help themselves instead of groveling before evil beings to obtain power. The Scientific and Industrial Revolutions were possible only with their unflagging efforts.
  • Safehold:
    • The Brethren of Saint Zherneau, with the goal to destroy the corrupt Path of Inspiration Church, and bring back the knowledge of humanity's true history.
    • The Circle, which wants to reform the Corrupt Church from within.
  • Star Trek:
    • The Kirk Cabal, founded by Starfleet Captain James T. Kirk in the novel Section 31:Cloak to oppose the rogue intelligence agency Section 31 . Learning of Section 31's existence and the damage one of their operations did to the fabric of space itself, Kirk forms a small cabal of like minded Starfleet officers to oppose 31. Over time the cabal recruited individuals like Elias Vaughn and Julian Bashir to oppose 31 and gather evidence to enable its eventual exposure to the public.
  • Victoria has a Monarchist International that secretly works to reinstate the imperial system of absolute monarchy in Germany and Russia, and backs reactionary paleo-conservative groups in the United States. They are still "benevolent" by comparison because, in this near-future dystopia, the current governments in these countries are all incredibly corrupt borderline dictatorships.
  • There Was No Secret Evil Fighting Organization has Amaterasu, which is more like a very eccentric country club than a conspiracy. It doesn't want anything from the public, it just wants to be left alone so it can pursue its (admittedly shady) goals in peace. Hence the secrecy. People want to know what Amaterasu is doing, but not by any stretch of the imagination do they need to know.
  • In Leia, Princess of Alderaan, Alderaan's leaders are in on the nascent Rebel Alliance, as are many of their staff. This being Star Wars, of course, one planet's government is small potatoes compared to The Empire, and the threat of Imperial reprisal is why they keep this under wraps. Leia herself, initially kept ignorant in the hope that that will save her if things go wrong, continually tries to discover more so she can help, sometimes causing trouble in the process, until eventually she's looped in.
  • In Star's Reach, the Rememberers' Guild is a secret society which finds, preserves, and copies important media from the past. When Plummer lets Trey in on the secret, he mentions that they release the media they've preserved to the public when it's most needed, such as reissuing a children's book with an uplifting message after a major conflict to remind the people of Meriga that there's more to life than war.

    Live-Action TV 
  • 30 Rock: The cast and crew of TGS have one to get Liz laid. She thanks them.
  • Babylon 5:
    • The heroes and their supporters form what they call a "Conspiracy of Light" against The Shadows' minions and pawns.
    • Sheridan was already part of one with his superior, General Hague, and other like-minded Earthforce officers who distrusted the new Earth Alliance President, Morgan Clark.
  • The Capture: Deconstructed. Everyone involved in "correction" thinks it's this, but everyone who's been affected by it has a naturally different perspective. It may cross over with Believing Your Own Lies. The activists' plot to expose them however could be seen as a straight example.
  • The watchers in Highlander. The greater good is writing a history book, but some members have their own agendas.
  • Stargate Command and its associated organizations, which fought and won three separate interstellar wars in defense of Earth without any Earthling not cleared being any the wiser. They've been known to protect the secret by simply beaming the evidence away, or by buying off a news company with the promise of an exclusive when the program goes public. Not to mention their diversionary tactic of backing a cheesy cable science fiction series about a secret government organization that roughly does exactly what Stargate Command does.
  • The eponymous organization in Threshold, which is trying to protect the United States (and, presumably, the rest of humanity) from an alien infection.
  • UFO (1970): The organization known as SHADO (Supreme Headquarters Alien Defense Organization) uses land, sea, and air units to intercept and destroy attacking/invading UFOs. It also acts to keep the alien attacks a secret, sometimes by erasing the memories of people who encounter aliens or UFOs.
  • The Warehouse Agents in Warehouse 13 are a secretive millennia-old organization that finds and hides artifacts so they can't harm anyone and so unscrupulous people can't use them.

    Tabletop Games 
  • The eponymous agency in Bureau 13 Stalking The Night Fantastic. It's a secret U.S. Government agency devoted to tracking down and dealing with evil supernatural forces.
  • The S.A.V.E. (Societas Argenti Viae Eternitata, or, The Eternal Society of the Silver Way) organization in Chill. It fights against dangerous creatures from the Unknown.
  • Delta Green. The eponymous group is an illegal organization inside the U.S. government that investigates and deals with Cthulhu Mythos related threats.
  • The d20 Modern setting has a few groups like this dedicated to protecting humanity from Shadows, the most prominent being Department-7, the one the PCs are most likely to belong to. The only known member other than them is a woman named "Ms. Fellows", who always speaks to them as a hologram (of a woman in a business suit and sunglass) at a studio apartment. Exactly where she broadcasts from is unknown, as is much of the details of the organization.
  • Firewall in Eclipse Phase is an inter-faction conspiracy dedicated to preventing the extinction of what's left of transhumanity at all costs.
  • The Company, of the GURPS setting Black Ops. Its members are part of a conspiracy of protection against a huge number of paranormal threats ranging from classic monsters like vampire and werewolves to ghosts, demons, dinosaurs and several different types of aliens all trying to prey on humanity in one form or another.
  • The Task Force VALKYRIE from Hunter: The Vigil is a secret branch of the US military, created to fight against supernatural threats and to enforce the Masquerade. Of course, they only appear benevolent from the mortal standpoint: the other critters of the New World of Darkness don't appreciate them much.
  • The Pentacle Orders from Mage: The Awakening. While as a whole they are more Gray, they want to make Sleepers mages, dethrone tyrannical Exarchs and their servants Seers of the Throne, and close the horrific Abyss.
  • The Orion Foundation of Top Secret:SI is an independent superspy agency that owes allegiance to no government, created to fight the sinister Web and frustrate its plans for taking over the world. According to the background materials from TSR, Orion's founders were survivors of the Web's early plots who pooled their knowledge and resources into fighting what they'd discovered.
  • BattleTech has Heimdall, an organization in the Lyran Commonwealth that was formed to battle the abuses of Loki, a branch of the Lyran government that has stepped way beyond their mandate all too often.
  • Grim Hollow: The Thaumaturge are about as benevolent as anyone in Etharis can be; a secret society of the most powerful mages on the continent, they're primary purpose is to stop evil magical monsters (like the Great Beast and the Aether Kindred) from running around unchecked, by whatever means necessary. If that means sacrificing the occasional small town to save a greater number of people, that's the kind of choice they'll make. That said, they also contain a number of explicitly evil members, including vampires from Ostoya. The main reason they don't due anything about the vampiric aristocracy running an entire empire openly is because some of those vampire are members who always vote against taking any action against the Crimson Court.

    Video Games 
  • The setting of The Alliance Alive is dominated by Obviously Evil tyrants, so La Résistance works in secret.
  • The Assassins in Assassin's Creed try to stop the Templars from installing a One World Order. On the other hand, the Templars have many Anti Villains and seem to think that Utopia Justifies the Means, but they have some questionable methods of reaching their goals (starting World War II, for example) and they believe that Humans Are the Real Monsters.
  • Most conspiracies in the Deus Ex Universe have some sort of benevolent goal, although this is usually a case of a group of conspirators believing themselves to be in the right. This can and does lead to multiple conspiracies with the same goal coming into conflict because they disagree on how to achieve said goal.
    • In Deus Ex, Morgan Everett tries to portray the Illuminati as this. And they kinda do come across as one when compared to the more immediate and malevolent conspiracy at hand, set in motion by their spin-off organization Majestic-12. In the "Join Illuminati" ending, Morgan and JC are rebuilding the world — however, Morgan reminds JC they have to do it through proxies.
    • Belltower's human trafficking operation is the only real exception; they are purely profit-motivated with no redeeming qualities whatsoever. Majestic-12 comes close, being only interested in power for power's sake by the start of the first game, but even they were created because they felt the Illuminati could be helping people more rather than simply observing the collapse.
  • In Double Homework, Daniela presents herself and Dr. Mosely/Zeta as this to the protagonist. Mosely herself does say that doing their work requires a conscience, and that they are working to solve a problem that could have unfortunate consequences if left unchecked. Still, Mosely tries to kill the protagonist and his friends when they become "liabilities".
  • The oldest military order in Guild Wars 2, the Order of Whispers, is a covert organization that manipulates politics to maintain peace within all nations using knowledge and secrets. They feature prominently as one of the organizations the player character can choose to join as well as being responsible for keeping the charr-human peace treaty intact, among many of their activities the player finds out about.
  • In Infra, there is a secret group called the "Raven Research Institute", which investigates corruption in the city of Stalburg, and in particular Stalburg Nuclear Weapons' illegal weapons trading schemes and their efforts to cover these up, which among other things had led them to murder the survivors of the metro train wreck. It is revealed that the player character's boss, Paul Lauwens, has a secret agreement to provide them with information, but the company's servers had been hacked, leading to the loss of data — which the player can recover by stealing the USB drive from the hacker's den right after the Pitheath sewage treatment plant.
  • The Healer's guild in Legacy of the Ancients is a front for a secret society dedicated to thwarting the Sealed Evil in a Can that the Wizard's Compendium represents. If you complete a quest to save the last of the Compendium's creators, he gives you a mark that alerts the guild of your quest and they assist you with help and information as best they can.
  • In Lily's Garden, Aunt Mary's husband Arthur De La Rosa had founded a Masonic-type loge called "The Order of the Ascending Eye" to investigate government corruption (although it is later revealed that the Order had since morphed into an elite, invitation-only chess club).
  • In Perimeter, the Exodus faction is an offshoot of the Freemasons who spearheaded the fantastic science seen in the game.
  • In Persona 3, the Kirijo Group was evil a few generations ago, but changes in management and several very karmic disasters purified it. The current leader of the Group wants nothing more than what is best for humanity, a goal that is not served by handing over responsibility for the Dark Hour to people who know nothing about it and can't fight Shadows themselves. By the time of Persona 4: Arena, Mitsuru Kirijo is taking steps to legitimize the Group's supernatural exploits (breaking the Masquerade to Japan's security agency, for example), but they're delayed by government corruption and victims of the previous Group going on a superpowered rampage. Basically, the Group has too much on its plate already to deal with P.R.
  • In Persona 5, the Phantom Thieves' magic is a lot more trustworthy than it looks, but only they have access to it, so they can't prove that to anyone. Also, the group consists entirely of people who the conventional system has already failed to protect, so they are unwilling to give Japan's "legitimate authorities" a chance to betray them again.
  • The Family in Resident Evil 6 is an organization dedicated to the preservation of global stability.
  • The three secret societies that the player can join in The Secret World generally have good intentions. The Templars are very upfront about their desire to defend mankind against occult threats. The Illuminati are more self-serving, but there's no way to get ahead and to the top of the pile if the whole planet has been destroyed. The Dragon have a more enigmatic end goal, involving a study of chaos theory and universal mathematical principles, but they still send agents to intervene in occult crises and protect humanity. Either way, it's generally agreed that, in a world where the paranormal is very real and knowledge of the occult can be used as a weapon to murder scores of people, letting its existence become public knowledge is a terrible idea that would lead to a proliferation of twisted cults serving evil gods like the Morninglight, supernaturally-enhanced terrorist attacks like the Tokyo bombing, and the Filth.
  • Star Wars: The Old Republic
    • The Star Cabal style themselves in this way, seeking to curb the Jedi and Sith Orders in general and their tendency towards massive, mutually destructive wars in particular. However, over the centuries, it has grown less noble; not only has it Jumped Off The Slippery Slope in a big way, its members have grown less concerned with keeping the peace and more concerned with how their access to massive resources and information on virtually everything in the galaxy can be used to improve their lives and/or bring down their enemies. After bringing down the Star Cabal, the Imperial Agent has the opportunity to use their Black Codex and "disappear" — erasing themselves from all records and becoming untraceable — in order to become a Benevolent Conspiracy of their own within the Sith Empire.
    • At the end of the Yavin IV arc of Shadow of Revan, there's a more-or-less official Benevolent Conspiracy formed between Jace Malcolm, Satele Shan, and Theron Shan, with the Player Character's involvement. They're an actual Republic joint task force investigating the reborn Sith Emperor but their real goal is basically to act under the Supreme Chancellor's nose if need be. The Chancellor isn't all that happy about this, but when the Supreme Commander of the Republic Army, the Grandmaster of the Jedi Order, and one of their most senior spies, who are coincidentally(?) husband, wife, and son, want to go off and conspire together there's not much you can do about it.
  • The Keepers from the Thief series. They're more apathetic than benevolent, but they're (in theory) dedicated to preserving Balance of Power. They just decided that not interfering was the best way to do it.
  • XCOM has the player as the head of the military division of a secret global initiative to defend planet Earth from invading aliens. Complete with a surprisingly affable Omniscient Council of Vagueness to report to.
    • XCOM: Enemy Unknown spells it out more: The "Extraterrestrial Combat Project" has been ready to go at the first sign of alien invasion for decades. The game starts by the Omniscient Council of Vagueness merely activating the X-COM project. We also get to understand that it's an International Government Conspiracy, and rather than being the ultimate big-wigs that gives XCOM orders, the Council of Nations is functionally more just secret patrons providing funding and personnel that XCOM answers to, but ultimately acts independently from. The main reasons XCOM remains covert instead of openly fighting against the aliens are 1) operational security and 2) political cover, as XCOM can only respond to so many crises at a time, and has more important things to be doing than public relations.
  • In Zero Escape, the espers of Crash Keys must constantly shift into alternate universes to get their work done, preventing threats that only other espers can see firsthand. Not much room for a social media presence in that...

    Webcomics 
  • In Homestuck, Skaia Net, the company that produces Sburb on B1 Earth, is old, powerful, and clearly well-intended. Its replacement on B2 Earth is significantly more dangerous.
  • Autumn Bay has the Shadowlight League, who are dedicated to the protection and training of wizards and sorcerers and protecting the world from esoteric threats.
  • El Goonish Shive: The mysterious government agency that Mr. Verres works for that keeps knowledge of magic hidden from the public. Mr. Verres has stated the reason for this is if people knew that magic existed, and that they could learn it themselves, then dangerous people will get magic too; people that you really don't want to give superpowers to. As it turns out, unknown to even the majority who do know of magic, Magic itself wants to keep itself mostly hidden, with only a few people knowing about it. If knowledge of it becomes too widespread, it will alter the rules of how it works, rendering (almost) everybody powerless. This has happened several times in recorded history already.
  • The Order of the Stick has the Sapphire Guard. Their order officially does not exist, and on the front these paladins serve as the Praetorian Guard. Their real purpose? To guard a "gate" that holds together the prison of an Eldritch Abomination. Actually, Azure City itself is a city-state built for this purpose.
  • Platformers has the Galaxy Council, formed by various deities or otherwise people in higher standing from the Platformers' home worlds, and its members are staunchly on the side of the heroes. The council consists of Eldstar, Polokus, Rosalina, L.O.G., the High Priestess and the Queen of Cress.
  • Parodied by Shen Comix, with the New World Order of Wholesomeness. They put chemicals in the air and water to make people more healthy and happy.

    Web Original 
  • The SCP Foundation isolates and contains threats to human survival and "normalcy" (and, by extension, life and the universe in general when possible). They're definitely a darker interpretation of this trope, but in the SCPverse, sometimes one's choices boil down to committing atrocities, or seeing humanity go extinct. The Foundation is ready and willing to commit those atrocities. Conversely, the motto of Secure, Contain, Protect includes protecting anomalies from the world if needed. There are many cases where the Foundation acts as a Fantastic Nature Reserve for entities and objects that The World Is Not Ready for, or which would be destroyed or exploited by other organizations. This is a frequent source of ethical conflict for the Foundation's staff as they find themselves sheltering things like unique and fascinating lifeforms... that happen to enjoy eating people.
    • The Foundation is opposed in principle by a second benevolent conspiracy, the UN-backed Global Occult Coalition (as opposed to the SCP Foundation, which is a N.G.O. Superpower), which is dedicated to the wholesale destruction of anomalies rather than their containment. As the name suggests, it's a coalition of 108 different occult organizations. One of them is the Illuminati.
    • Two more frequent Foundation opponents, the Serpent's Hand and the Manna Charitable Foundation, both have benevolent goals. Unfortunately, the MCF doesn't think its plans through before enacting them, and the Serpent's Hand can't achieve its goals without shattering the Foundation's Masquerade.
  • RWBY: Ozpin leads a secret cabal of Huntsmen within and allied to the four great Huntsman Academies to hide the true history of Remnant, the Ancient Evil they're fighting, and the four divine Relics they're protecting. They maintain secrecy out of fear of global panic should the Awful Truth ever be revealed, which would trigger hordes of Grimm to assault the last remaining bastions of human civilisation. However, with Ozpin keeping secrets from even his inner circle and several of his allies pursuing their own vested interests, Teams RWBY and JNPR find themselves increasingly at odds with adult old guard and eventually take matters into their own hands to fight the Big Bad on their terms instead.
  • Majestic-12 is presented this way in Magic, Metahumans, Martians and Mushroom Clouds: An Alternate Cold War. As opposed to the malevolent aims usually presented in conspiracy theories, it's made clear that the shadow government they're tasked with setting up is an emergency contingency to ensure continuity in case the main government is ever decapitated by the Soviets or hostile aliens.

    Western Animation 
  • The Illuminati of Gargoyles at least think of themselves as this. But we don’t know if it’s true, and some of the members really aren’t helping their case.
  • In Transformers: Prime, Team Prime and the US government secretly work together to defend the Earth from Decepticon invasion. The Autobots also share their advanced technology with humanity in exchange for a safe home and logistical support in defending the human race.
  • In the South Park episode, "Mystery of the Urinal Deuce", the government didn't start 9/11, but they created the 9/11 conspiracy movement. They did it because they don't want to appear as a nation weak enough to let such an attack happen, the movement giving them an illusion of power to some.
  • The eponymous organization in Codename: Kids Next Door qualifies, as Adults Are Useless in this setting, and often evil. (Of course, the KND themselves edge close to the He Who Fights Monsters line at times.)
  • Gravity Falls: The Society of the Blind Eye are a secret society of ordinary townsfolk who are dedicated to upholding the Masquerade, using a memory-wiping gun to erase people's memories of encountering anything supernatural in the town or surrounding forest. However, they're doing this only for well-intentioned reasons, as they believe that people are so traumatized by the existence of the paranormal that they're better off without knowledge of it. To be fair, they erase their own memories of any such encounters as well.


 
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Gravity Falls [Blind Eye's M.O]

Scene from Gravity Falls, Ep 27, Society of the Blind Eye. Dipper, Mabel, Wendy and Soos go to help McGucket, the town's resident crazy person, restore his memories in the hopes he can lead them to the author of the journals. Their search has them stumble upon an odd organization called the Society of the Blind Eye. However the four end up captured and soon meet their leader, Blind Ivan, who explains their purpose.

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