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- Cowboy Bebop has The Syndicate, a group of Mars-base Chinese Triads which employed series protagonist Spike Spiegel as a hit man and also employed Big Bad Vicious up until the point that he took over the organization and turned it into his own personal army to satisfy his Blood Knight appetites.
- The Authority, with the titular superhero group.
- The Boys, with the titular group of CIA black-ops Cape Busters.
- The Enclave: A group of criminal scientists in the Marvel Universe.
- The Committee: A criminal organisation from the same.
- The Conclave: The Avengers foes. A shadow cabinet made up of members of every U.S. government organization.
- The Corporation: Nationwide business-like criminal organization. Foes of Captain America and The Incredible Hulk, amongst others.
- The Cabal, a group of several powerful supervillains and antiheroes, and Evil Counterpart to The Illuminati.
- Magento's organization was just called The Brotherhood for a while. After it abandoned The Brotherhood of Evil Mutants.
- The Fraternity from Wanted; while the movie has an organization of Anti-Hero Jerk Ass assassins, the original comicbook has full on amoral supervillains.
- Sin City has "The Guild", a group of assassins who also deal in the Black Market.
- The Core Line setting has The Foundation, which is the result of both The Foundation For Law And Government and the Phoenix Foundation pooling their resources (and getting assistance from people like Optimus Prime, now the Governor For Life of the State of Michigan) because individually they were too under-powered and under-gunned to make any change on the titular World Gone Mad. While many other organizations in the setting have the name "[Something] Foundation", the moment you hear "The" Foundation is out to get you, you should seriously think about pulling stakes and running.
- The Division in Push, who are a Mutant Draft Board looking to harness all of the powered people of the setting as human super weapons.
- The Order from Sherlock Holmes are a No Celebrities Were Harmed version of the Freemasons as they were commonly thought of in Victorian times, being a shadowy group of influential men at the highest reaches of power engaging in mysterious, weird rituals. It's gradually taken over by a powerful and charismatic Dark Messiah who has returned from the dead and is demonstrating his power to such an extent that almost the entire country is utterly terrified of him. However, it's ultimately a complete deconstruction, as the Order is largely presented as a bunch of superstitious and largely ineffectual old men who are utterly caught up in their own mythology to the extent that they'll let the so-called Dark Messiah, in fact a complete charlatan, seduce them with a theatrical manner and some admittedly pretty clever conjuring tricks. Hey, this is Sherlock Holmes; as if he wasn't going to be Doing In the Wizard. It's also an excuse for them to have orgies, apparently.
- The "Human Project" in Children of Men are a group of scientists dedicated to curing infertility, supposedly based in the Azores. They are secretive to the point of being a myth.
- 1984 has The Party. (It also has The Brotherhood, but they're not working against the protagonist.)
- In the Anne Rice books, it's The Talamasca. "We watch, and we are always there."
- Bentley Little has a whole slew of novels like this. The Store, The Association, etc. They are all horror.
- The Majestic 12 from Scarecrow, the 12 richest men who secretly run the world for their own profit.
- An earlier Matthew Reilly book Area 7 had Die Organisasie (The Organisation in Afrikaans), a group of South African leftovers from Apartheid.
- The Shop, from Stephen King's Canon Welding crossover-verse which ties all of his fiction into The Dark Tower universe.
- The villainous secret organisation from the Mediochre Q Seth Series is known only as The Organisation Which I Represent.
- The Dominion from Star Trek: Deep Space Nine has the right sort of name (although, so does The Federation, come to think of it), and they were definitely a mysterious powerful organization in the first few seasons. Section 31 is the clandestine intelligence agency in the Federation that has been around from the beginning. The Circle was a short-lived Bajoran political party/terrorist organization/Cardassian front. Not to mention the Obsidian Order of the Cardassians, and Romulan Tal Shiar.
- Stargate SG-1:
- The N.I.D. According to the RPG sourcebook it stands for National Intelligence Department.
- And later, the Trust, a group of incredibly powerful industrialists that was taken over by the Goa'uld.
- Bureau Thirteen in Babylon 5. Heard of once in the episode Spider In The Web, then never heard from again.
- Parodied by the Agency from the Sci Fi Channel's series The Invisible Man. It's a secret government agency that consists of about five (visible on-screen) people, and because of this is prone to being transferred around between various departments of the US Government, as well as suffering from budget cuts. About the only thing they have going for them is that the titular invisible man works for them.
- Anthony Perish and Tony Mokbel refer to their criminal organisations as The Company in Underbelly: Badness and Fat Tony & Co, respectively.
- "The House" from The Player.
- The Directive, a shadowy intelligence organisation from the Aberrant role playing game.
- The Cabal in Blood. Known more properly as the Cult of Tchernobog, but more often called just Cabal.
- The Exchange from Knights of the Old Republic, an interstellar criminal organization, although in at least one incident in The Sith Lords they work under a non-too-subtle cover organization called "The Bumani Exchange".
- The Order in Freelancer. Subverted in that they're actually the good guys, fighting off a race of shapeshifting aliens called the Nomads.
- The Hitman video games have the International Contract Agency, which is usually known as just The Agency. Although they're the organization the protagonist works for, they're morally ambiguous enough to count. A competing group from Hitman: Blood Money is The Franchise. In the first movie the group is called The Organization.
- The Organization from Street Fighter III, a strange, powerful cult that has produced the superhuman Gill, is never really given a name in the Japanese, though it is sometimes referred to as the Illuminati in English.
- The Agency from the Syphon Filter series of games, which served under The Consortium. After the protagonist becomes the new leader at the end of the third game, it gets reorganized into the International Presidential Consulting Agency... which still doesn't have any proper nouns.
- The Foundation in The Suffering II: Ties That Bind, which seems to be a paramilitary organization hell-bent on capturing Malefactors and supposedly researching them. They also have an unhealthy interest in Torque, because they work for Blackmore.
- In Kingdom Hearts: Chain of Memories, before their true scope and motives were revealed, Organization XIII were simply referred to as "the Organization".
- The Star Cabal in Star Wars: The Old Republic, a shadowy organization that butts heads with the Imperial Agent throughout their storyline. The Cabal is revealed to have been manipulating events since not long after the Great Hyperspace War (ca. 1200 years before the game) and several characters from other class missions have cameos among their ranks, leaving it ambiguous how much they actually did in the interest of their long-term goals.
- In early episodes of Phineas and Ferb, the organization Perry the Platypus works for is known simply as The Agency. In later episodes it's officially known as O.W.C.A., the Organization Without a Cool Acronym.
- The Centre from Martin Mystery is a clear cut heroic example.
- On Ben 10, the Forever Knights were originally called The Organization.