Cloak and Dagger

Spy Agencies in Real Life are largely dull bureaucracies that exist to gather minute amounts of detail together, then sorting through the vast hoards of it for anything interesting they might come across. Ian Fleming and the Cold War as a whole managed to change that perception by creating a vast horde of glamorous secret agents devoted to fighting for Queen and Country (or whatever nation they belonged to).

Cloak and Dagger groups are essentially those involved that have no real relationship to existing organizations but exist merely to conduct this kind of clandestine fun.

See Fictional Counterpart for examples of how many groups attempt to skirt around real world Geopolitics. See also Spy Fiction. A Sub-Trope of Government Agency of Fiction.

Not to be confused with the Marvel Comics characters Cloak and Dagger, the MCU TV series based on them, or the 1984 spy adventure film starring Dabney Coleman.

Anime and Manga

 * The Black Organization in Detective Conan seemed to have this going on, but subverted by some of its members decided to still have relationships and friendships. Others see each other as tools (Gin).
 * The eponymous Absurdly Powerful Student Council of Best Student Council is so powerful that it has its own intelligence unit, Covert Squad.
 * Of course, England from Axis Powers Hetalia would be the best spy for the allies.
 * Princess Principal: We never learn whether Control is the name of the main characters' spy agency or just the name of the people in charge of it. The team we see is officially named "Team Principal", but they call themselves "Team White Pigeon".

Comic Books

 * Checkmate in the DC Universe is part of the greater Department of Metahuman Affairs and has a chess motif.
 * SHIELD is a fictional agency employed by the United Nations (and formerly, the US government) to fight terrorists.
 * Also, the S.W.O.R.D. and now, (the) H.A.M.M.E.R.

Film

 * The SPECTRE of James Bond had a short run in the Ian Fleming novels and was Bond's full-time archenemy in the movies for a while. Effectively, it is the first known example of a Rogue Intelligence agency devoted to its own profit.
 * The organization Quantum has filled it and SMERSH's role for the Daniel Craig Bond movies.

Literature

 * The titular organization of Tim Powers' Declare, in which an agent's catechism includes the question, "Would you fight magic with magic?"
 * The Bureau, the 'deniable' British intelligence service of the Quiller series by Adam Hall.
 * Kim is more realistic, but the "dagger" part shows, especially around Mahbub Ali. He's still annoyed to no end when someone tries to kill him and it's not personal.

Live-Action TV

 * Airwolf had The Firm despite it being obvious that it was the CIA.
 * Alias had SD-6 and an increasingly large number of strange terrorist organizations arrayed against it.
 * Control from Get Smart is one such example, as is its counterpart Kaos.
 * La Femme Nikita was characterized around an organization known as Section One.
 * The Man from U.N.C.L.E. is another said example.
 * Section 31, the Tal-Shiar and the Obsidian Order are the cloak and dagger organizations of the Federation, Romulans and Cardassians. One episode of Stgar Trek: Deep Space Nine, however, shows Bashir and Garak (The first is British, the second is an actual spy) stuck in a James Bond-style holo-program. When Bashir says that he is under cover as a rich playboy, Garrak says that he joined the wrong intelligence agency. Mostly played straight otherwise, though Section 31 serves more to raise the question of whether it is okay to betray your principles in order to preserve it than anything else.
 * The Good Guy agencies on Chuck are nominally the CIA and the NSA, though they bear little resemblance to their real-world counterparts. The Bad Guy organizations, Fulcrum and the Ring, seem largely made up of rogue espionage agents.
 * The Canadian series Adderly never did make quite clear whether "ISI", International Security and Intelligence, was a US, Canadian, or bifederal agency.
 * In the 2010 Nikita, the government agency Nikita used to work for is called Division.
 * The organization of burned spies in Burn Notice.

Tabletop Games
"Ed Greenwood: But there's another sort of secret society that we can't spotlight in the rules [...] : We ruin its secrecy by talking about it. These small, local, lowdown cabals of crooked merchants are a vital, ongoing, many-layered (as in "You shouldn't have just one at a time") part of the "home" Forgotten Realms campaign, and in many, many lively, long-running D&D campaigns set in any world. They're just the thing for framing or hiring PCs and plunging them throat-deep into unexpected and usually unwanted adventure."
 * Forgotten Realms, due to the nature of this setting, has a lot of secret and semi-secret organizations ranging from information brokers to assassin guilds to Hero Secret Service groups. The most important ones made it into a Sourcebook quite appropriately named Cloak & Dagger.

Video Games

 * City of Heroes has the Malta Group, a international coalition of intelligence agents formed during the Cold War to get around their governments' unwillingness to conscript superheroes into the intelligence community.
 * Metal Gear: FOXHOUND, anyone?
 * Team Fortress 2: Reliable Excavation Demolition, meet Builders League United. Possibly a subversion in that neither group has any real idea what they're fighting for or why they would need a small, color-coded briefcase from the opposing company.
 * The name is referenced by the Spy class weapon "Cloak and Dagger"
 * The Spy's official class role, as given in the original 2006 gameplay trailer, is "Uncloak and Dagger".
 * The Office of Naval Intelligence in Halo, best known for creating The Hero, Master Chief.
 * And it's named after a Real Life agency with much more mundane objectives.
 * The VCI from Alpha Protocol seem to work mostly by blowing things up. The G22 are a wee bit more discreet, but still do more ass-kicking than data-milling. The eponymous organization exists to carry out missions that the United States doesn't want to be officially involved with.
 * While G22 and Alpha Protocol have no excuse, the VCI is actually a mercenary organization, not an espionage organization.

Web Original

 * Each of Open Blue's major nations has one of these.
 * In the Global Guardians PBEM Universe, this is the function of Tarot's Wands Division. One CIA analyst compared the Wands to "the KGB in the good old days of Communism... except the Wands have supervillains."

Real Life

 * SMERSH was a Real Life agency. It was a subsection of the then-NKVD during World War Two, whose existence was devoted to halting espionage within the USSR. The organization was disbanded—officially, that is—shortly after the end of the war, but Ian Fleming appropriated it and used is as what amounts to a terrorist organization funded by the KGB.
 * Real Life spy agencies often have very little to do with their depictions on television or in other media, in small part because of ignorance but also because real life spy-work is rarely so glamorous. Some fun facts that have been ignored by the media are:
 * The real-life portfolio of the U.S. National Security Agency is signals intelligence and cryptanalysis (codebreaking). That hasn't stopped screenwriters and others from depicting "NSA agents" engaging in espionage fieldwork which in reality would be handled by personnel of the CIA, FBI, or various military intelligence agencies.
 * Examples: "Jinx" Johnson (Halle Berry) in Die Another Day, Xander "Triple-X" Cage (Vin Diesel) in xXx, and John Casey (Adam Baldwin) on Chuck; none of whom seem to be information analysts as their primary role (Cage and Casey are specifically recruited as adaptive enforcers).
 * Fridge Brilliance sets in when you realize that since the NSA is publicly only charged with cryptography and electronic surveillance, it could easily deny involvement should any of its off-the-books field agents be caught.
 * The KGB in real life are often called "Dzherzhinsky Square", after the street where the headquarters are located (which in turn is named after the first head of its predecessor, the Cheka). (Lubyanka is a prison). They are also generally depicted as much of the power and nightmarish disregard for life as the real life NKVD, their predecessor in the Stalin era. To be fair, the real life organization wasn't smiles and roses for as long as it existed anyway.
 * MI6 is actually an agency called SIS, with James Bond being treated as the most Egregious producer of this inaccuracy. It hasn't been called that since World War Two, well before Ian Fleming served. The agency now has to use the title in its recruitment advert.
 * MI5, its counterpart which deals with internal subversion and such matters, is actually just the Security Service. so the... SS.
 * Because of this, it tends to be referred to as the British Security Service.
 * Which would, then, make it the BS...S?
 * Since the unification of the armed forces, this is properly DI5.
 * This comes up in an episode of Yes, Minister, where Sir Humphrey tells Hacker that MI5 does not exist, and if it did exist, it would be DI5, which does not exist either. (Although, of course, everybody knows it exists, the government does not admit it publicly.)
 * Contrary to popular belief, Canada does have its own intelligence agency, called C-SIS (Canadian Special Intelligence Service). As with most Canadian agencies, it doesn't get much publicity. The girl at the end of Quantum of Solace is the only one that comes to mind.
 * A Season 4 episode of Stargate Atlantis went to great lengths to point out how "stupid" a name C-SIS was for an intelligence agency ("That's the best you could do?"), but this is also completely in check with the rest of the tongue-in-cheek Canadian bashing on the show (most of the cast and crew is Canadian, and the entire franchise is filmed in Vancouver).
 * What the US vaguely terms "Covert Action" is at the borderline of intelligence work. It is not the same but clandestine services may do this as well as straightforward espionage or even have a special department tasked with it not least because some of the technique is similar. Alternately it might be tasked to military special forces. Sometimes even both the military and the spies have a finger in this. Covert Action includes a wide variety of things like secret diplomacy with a polity whose sovereign status is unrecognized (like a tribe or a rebel group). Or it could mean paramilitary operations like a long period of cooperation with a given faction. It is vaguely tied to commando operations because everything about this is vague. This sort of thing has some resemblance to the James Bond or MacGyver kind of secret agent.