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Anime & Manga
- 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.
Live Action TV
- 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.
- 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.
- 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."
- The Avengers: In a New Avengers 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.
- Section 31 from Star Trek.
- Agents Of SHIELD 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.
- 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".
- In Isaac Asimov's classic collection, I, Robot, there is a covert group who sees the control given to the AIs as creating a Vichy Earth where humans are enslaved to machines. The machines should be able to predict and compensate for the discrepancies these small acts of sabotage produce, but they aren't.
- In almost all Urban Fantasy, all the creatures are part of a covert group. For example, 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.
- There's a covert group of wicked witches in Roald Dahl's The Witches; it exists expressly for the purpose of wiping out every single child on Earth.
- 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.