Secrets and things done secretly are interesting. Thus, many fictional groups—both heroes and villains—act as covert groups: groups that act undercover and aren't known to many outsiders.
Often, a covert group is engaged in controversial or outright illegal activity, as otherwise there would not be any reason for secrecy. In a Government Procedural, these groups also act in sensitive matters such as national security.
Part of many a Conspiracy Theory, The Conspiracy and Government Conspiracy. Often employs The Men in Black, No Such Agency, Unusually Uninteresting Name, Resignations Not Accepted, The Masquerade or the Covert Group with Mundane Front to keep itself undercover.
Related to Government Agency of Fiction.
- In Murasakiiro no Qualia, JAUNT is exactly this. A mysterious group that nobody knows about, apparently backed by the Amaerican government, which has no qualms with stealthy blowing up airplanes to keep their secrets... secret.
- The Livewires are a covert group of Badass Automatons.
- In X-Force, its team was portrayed as a covert group under the leadership of his character Pete Wisdom starting in 2000.
- Justice League of America: A covert ops group with technology-based powers working for the U.S. government tries to eliminate the world's superhumans.
- The Secret Avengers have been this for the Avengers.
- MONARCH, a top-secret government organization from Godzilla (2014). Their original purpose was to keep the existence of Godzilla and the M.U.T.O.s a secret to the public.
- James Bond: SPECTRE and its mysterious leader Ernst Stavro Blofeld is behind many criminal schemes involving Evil Plans of the Take Over the World variety. And its ruling council is a behind-the-scenes cabal of corrupt officials, politicians, terrorists and businesspersons SPECTRE is essentially a shadow government, whose members choose to operate in the dark.
- Area 51: The series deals heavily with these. In the first book there is Majestic-12 (alias Majic-12) and its security/black ops Nightscape. Later books soon introduce more, like Section Four (Majic-12's equivalent in the Soviet Union, then Russian Federation), STAAR, The Mission and more. Most are nefarious, others not entirely.
- Isaac Asimov's "The Evitable Conflict": The Society of Humanity is a semi-public group who sees the control given to the AIs as creating a Vichy Earth where humans are enslaved to machines. The machines prove capable of predicting and compensating for the discrepancies their small acts of defiance produce.
- Roald Dahl: There's a covert group of wicked witches in The Witches; it exists expressly for the purpose of wiping out every single child on Earth.
- In The Dresden Files, Harry is part of the White Council, a covert organization of wizards that contends with other covert groups of faeries, vampires, and demon-possessed sociopaths.
- Various covert groups wage the titular conflict of the The Silent War. The Brotherhood of the Pit are the remnants of a nation of evil sorcerers, the Night Hand is a cult devoted to the slumbering Death Lords, and the Shades are a remnant of the fallen nation that opposed both of them. Since the last great, open war three centuries earlier the fight has stayed in the shadows.
- Agents of S.H.I.E.L.D. is replete with covert groups, starting with S.H.I.E.L.D. itself, which somehow manages to stay covert despite having logos on their vehicles and frequently taking action in crowded public places. That is, until another covert group, HYRDRA, reveals itself after being embedded within S.H.I.E.L.D. since its creation, and all hell breaks loose.
- New Avengers: In one episode, Soviet spymaster Ivanov planted many undercover agents in Great Britain, where they wormed close to tactically important persons, ready to assassinate them on cue. This covert network was called "the House of Cards," because select playing cards would activate the moles. British Avengers John Steed, Purdey and Mike Gambit thwarted Ivanov and neutralized his moles.
- By Any Means was about a covert group whose job it was to find legal means to punish those who had escaped justice for their crimes. A Running Gag that was whenever they were asked if they were cops, the response was always "It's a grey area".
- La Femme Nikita has Section One, where the main character works.
- The Impossible Mission Force from Mission: Impossible routinely takes on covert operations while shielding Washington from culpability. "Should you or any of your I.M. Force be captured or killed, the Secretary will disavow any knowledge of your actions."
- On Nikita, a main plot point is a secretive U.S. government agency known as "Division" has for years been recruiting young adult convicts by faking their deaths and forcing them to train as spies and assassins.
- Our Miss Brooks: In "Deacon Jones", Miss Brooks, Mr. Boynton and Walter Denton meet secretly to rehearse for a job with the hillbilly troupe led by the eponymous deacon.
- The Watchers in Highlander probably count. Theyre a secret society which observes and records the battles of immortals and helps to hide the headless bodies so the immortals stay hidden. They take an oath not to interfere, although a couple broke the oath. Joe Dawson became good, if sometimes rocky, friends with Mac and interfered a few times to stop something bad from happening, and another watcher was in love with his assignment and helping him win.
- Star Trek: Picard: The existence of the Zhat Vash is kept secret not just from the general public, but the Tal Shiar as well. Zhaban, who was once a member of the Romulan Secret Police, dismisses the ancient cabal as just a myth to frighten new recruits. However, Picard later discovers with Laris' help that the Zhat Vash is indeed real, and this shadowy group is The Unfettered to an even greater degree than the Tal Shiar.
- The eponymous Alpha Protocol, as well as the G22.
- Assassin's Creed features many covert groups. Besides the Templars and Assassins, there are also the Hermeticists / Hermetic Order of the Golden Dawn, hacker collective Erudito, and the Initiates.
- The eponymous XCOM and (in the remake, at least) the Council of Nations supporting the project. The remake also has the opposition E.X.A.L.T.
- Evolve has Counter Intelligence Group 9, a government organization within Hub. While they still have a layer of sci-fi to them they take part in actions reminiscent of real life groups, such as using deep cover agents to begin a war in another nation so they could take advantage of it.