From a show, film or book.
Some of mine are:
The Men in Black from the MiB franchise.
The Impossible Mission Force (IMF) From the Mission Impossible franchise
The Counterterrorist Unit (CTU) from the show 24. But only if Jack Bauer is there. haha
EVIL Corp from Mr. Roboto.
shareOcp from Robocop.
shareWarehouse 13 from the show of the same name.
shareKAOS from Get Smart
shareThe Ministry (or Ministry of Elite Intelligence) - The Avengers (tv series). The head of the Ministry is referred to as "Mother." Gotta love that.
CONTROL - Get Smart (tv series). Biggest nemesis: Kaos.
Impossible Missions Force (IMF) - Mission: Impossible (tv series; I'm not very familiar with the movie franchise)
SPECTRE (Special Executive for Counter-intelligence, Terrorism, Revenge and Extortion) - James Bond nemesis. Blofeld one of best villains. Not really an "agency" as such, but acts like one.
Nemesis - From the short-lived TV series The Champions. A United Nations law enforcement organization based in Geneva.
Spectrum - Captain Scarlet (tv series)
World Security Patrol - Stingray (tv series)
World Space Patrol - Fireball XL5 (tv series)
The Watchers - Highlander: The Series
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