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Anime and Manga
- Hellsing has a serious examples of various Church Militant groups opposed to one another.
- Also serious: Darker Than Black has constant infighting between intelligence agencies of all kinds, mostly to find out more about contractors and the Gate. However, the whole situation was actually set up to keep the contractors too busy fighting each other to realize that PANDORA was planning to obliterate them.
- The Trope Namer is the famous MAD comic Spy vs. Spy which featured black and white trenchcoat-clad agents always trying to kill one another for no apparent reason. Occasionally a third spy, Lady Grey, would make an appearance and foil the both of them.
- S.H.I.E.L.D. vs HYDRA. And AIM. And RAID. Sheesh.
- W.A.S.T.E. vs E.M.P.I.R.E. vs M.O.T.T vs X.S.M. all to to be found in the pages of Matt Fraction's Casanova.
- Spy Boy has S.H.I.R.T.S. (Secret Headquarters International Reconnaissance, Tactics, and Spies) versus S.K.I.N.S. (Supreme Killing Institute).
- Clearly inspired by Get Smart (below), the modern Blaxploitation parody Undercover Brother has the black organization BROTHERHOOD facing "The Man".
- Combined with Murder, Inc. in Mr. & Mrs. Smith which features opposing groups of assassins.
- Our Man Flint. The movie featured a clash between Z.O.W.I.E. (Zonal Organization for World Intelligence and Espionage) vs. Galaxy (a parody of SPECTRE).
- In a very strange way, this is how angels and demons tend to operate in Good Omens, as personified by Friendly Enemies Crowley and Aziraphale. Their situation is explicitly compared to two spies in the middle of nowhere who've been essentially forgotten by their respective governments.
- Happens in some Tom Clancy novels, most notably The Cardinal of the Kremlin.
Live Action Television
- One of the most influential versions was that in Get Smart where the good guys CONTROL faced off against KAOS.
- Like the comic book counterpart, Agents of S.H.I.E.L.D. runs on this especially during the last one third of the first season. This S.H.I.E.L.D. VS Hydra kicked in to high gear when Season 2 came.
- The Man From Uncle. had U.N.C.L.E. vs. THRUSH.
- Alias had several, all non-humorous. First was CIA versus SD-6, then CIA versus Covenant, then CIA versus whatever Irina Derevko's network was. Plus there were other spy groups, like K Directorate, that worked against the CIA and SD-6.
- Chuck has a lot of this as well: CIA vs Fulcrum, CIA vs The Ring, CIA vs Volkoff Industries...
- The Game (UK TV) has 'Daddy' and his MI-5 team vs the Soviet spy 'Odin' and his henchmen.
- MI High had M.I.9 versus S.K.U.L. (originally) and K.O.R.P.S. (in the later seasons).
- Lancelot Link, Secret Chimp has A.P.E. (Agency to Prevent Evil) versus C.H.U.M.P. (Criminal Headquarters for the Underworld's Master Plan).
- That Mitchell and Webb Look had a James Bond parody facing off against a Le Chiffre parody, both being fed lines and info by agents... who turned out to be the exact same guys in a van.
- Team Fortress 2 uses this basic framing device (with the heroically-evil RED and evilly-heroic BLU) to provide the deliberately flimsy rationale for the game.
- Additionally, as Spies are one of the selectable classes, it literally becomes Spy vs. Spy in some cases.
- The ACME Detective Agency and V.I.L.E. in the Carmen Sandiego games. ACME is basically a Brand X version of Interpol and V.I.L.E. pretty much just exists to be evil. Or to feed Carmen's ego, Depending on the Writer. They aren't exactly spy organizations, but the series borrows tropes from the spy genre enough that it really doesn't matter.
- Ace Attorney Investigations is basically built around Interpol (represented by Lang and Franziska vs. the smuggling ring, although Edgeworth seems to be the only one who does any actual detectiving. With the exception of Lance (whose father is tied to the group and was Lang's real target all along), every single culprit in the game is a member of the smuggling ring.