Frequently, a [[TheHero Hero]], (especially an OrdinaryHighSchoolStudent) who gets his powers by accident or is granted them by some other force, will meet and be recruited by the Army or an equivalent which wants him to use his power for the good of the world. After a few {{Filler}} episodes pass by in which TheHero gets to hang out and bash monsters with their new best pals (bonus points for alienating their usual group of friends in the process), [[ForeShadowing several hints]] and [[BatmanGambit a few subplots]] will start to appear that cast the intentions of [[TheOmniscientCouncilOfVagueness "The Organization"]] into doubt. They will attempt to coerce the hero into doing morally questionable things (maybe [[SlaveToPR discrediting him or branding him a heretic]], [[TheEvilArmy inappropriate use of force]], or [[BroughtDownToNormal threatening to take away his powers]]), and they will be doing some ''other'' [[KickTheDog evil deeds]] that betray the mission or ethics the company once proudly touted as "elevating it" above mere [[TheMenInBlack Men in Black]].

Usually this comes as a shock to the member who first met and recruited the hero, as s/he and most of the junior officers are earnestly good people. Usually the organizations as a whole are not really evil, there are only a few corrupt members [[CorruptCorporateExecutive (usually higher ups)]] who try to abuse their power, only to be defeated by the hero, of course. After that problem has been cleaned up (often with an astonishing lack of the organization falling to infighting in the wake of such an obvious coup) he is then accepted as a legitimate member with full rights to their powers.

Minor and major variations of this plot can be found in many different media, for all it seems to be a pretty new convention. Contrast GoodAllAlong, VillainWithGoodPublicity.

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!!Examples:

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[[folder: Anime and Manga ]]

* In ''DigimonTamers'', the Hypnos organization really wasn't evil, they were just working on the government's behalf due to legitimate concerns - Yamaki is the only one who takes it personally. After it turns out Hypnos was doing more harm than good and they realize the Tamers are humanity's best hope, they turn things around and are vital to the heroes up to the very end of the series. Yamaki himself has a total change of heart and becomes the kids' strongest and most vocal supporter.
* This becomes the entire second {{Arc}} of ''Manga/{{Bleach}}'' once the OrdinaryHighSchoolStudent protagonists, the setting and basic premise are established. The full brunt of Soul Society's CelestialBureaucracy is brought to bear against the heroes: lower officer Rukia because her emergency illegal act was declared an executable offense by the [[spoiler:assassinated and secretly replaced]] Central 46, and the human kids because they try to protect Rukia from arrest and execution.
* ''TheLawOfUeki''
* ''BusouRenkin'', though without any actual evil or corruption going on - [[spoiler: the Alchemist Army tries to kill Kazuki because he will eventually become, after ''six weeks'', a [[PersonOfMassDestruction tremendous threat to everyone around him]].]]
** [[spoiler:And Kazuki actually agrees with their logic - he just didn't want to be executed immediately. He had been willing to spend 5 weeks, six days investigating possible cures, and then allowing himself to be killed if he hadn't found a way to stop or delay the transformation by that time. The Army decided they couldn't risk their estimates being wrong or Kazuki having a change of heart a few weeks down the line.]]
* ''ElementalGelade''
* ''Manga/DeadmanWonderland''
** It should be noted though that ''because'' it is Deadman Wonderland, any organization that doesn't involve actively torturing someone can be considered a good thing. No, seriously. Even use of anaesthetic puts you on 'the good guys' side.
* ''Manga/{{Claymore}}'': most of the Warriors of the Organization believe that they are trained to defend humanity from the yoma. They generally run the gamut from the more idealistic (like Jean and Deneve) to those who simply regard it as a job (Galatea and Theresa) with a few psychopaths like Ophelia in the mix. [[spoiler: Most Warriors are ignorant of the fact that they are essentially a biological weapons experiment and that the Organization itself creates the yoma. Some of them who find out decide to take the Organization down for this and other personal reasons.]]
* Chronos in ''Manga/BlackCat''.
* ''WitchHunterRobin'' does it. Solomon has national branches all over the world, and as a whole is fairly draconian since it kills witches, rather than capturing them like the Japanese branch [=(SNT-J)=]. [[spoiler: However, Solomon will not use inhumane experiments or genetic engineering, both of which the Japanese branch is heavily involved in. This is particularly subversive, since it seemed more humane, but its experiments on the witches it captures are [[{{Aesoptinum}} cruel and madness inducing.]] In a variation, Robin is never truly acquitted by the organizations, but her father figure and leader of Solomon does forgive her, while asking for her forgiveness.]]
* ''MartianSuccessorNadesico'', in which the Nadesico crew gets jerked around by factions within both Nergal and the UEDF.
* This is almost exactly what happens to NERV in ''Anime/NeonGenesisEvangelion'', except that Shinji, Misato and other initially-clueless-but-generally-good members do ''not'' prevent the higher-ups from completing their plans of questionable morality (well, at least Ritsuko tried to).
* In ''Manga/FullmetalAlchemist'', we eventually learn that [[spoiler:the entire state military is in fact a tool for the evil Homunculi, one of whom is in fact the ''head'' of the military. [[NamesToRunAwayFromReallyFast Though really,]] he is called ''[[PuttingOnTheReich the Führer]]''.]] Idealistic members try to stop them from succeeding.
* A somewhat darker variant appears in ''DarkerThanBlack'' -- TheSyndicate employs Contractors, but it ruthlessly uses those under its control to do all manner of dirty work for its own inscrutable benefit (and the Contractors are under no illusions concerning their work). Ultimately, the syndicate turns out [[spoiler:to have an agenda involving exterminating the contractors as a whole by closing Hell's Gate ([[LaResistance Evening Primrose]] beat them to Heaven's Gate). Both Hei, his TrueCompanions, and November 11 become examples of this trope when they find out, and in the latter cases Conspiracy RedemptionEqualsDeath.]]
** The Syndicate is an interesting play on this trope, as on the surface it appears to be merely a criminal organization, while in reality it's [[TheManBehindTheMan controlled by]] [[spoiler:the UN, as are most of the supposedly opposing groups]].
* In the ''SonicX'' continuity, the military organization G.U.N (Guardian Unit of Nations) was responsible for the attack on Space Colony Ark fifty years ago, during which twelve year old Maria Robotnik, amongst many others, were killed: the incident was fobbed off as an accident and everyone who was connected or suspected of connection was either killed or discredited. Leaping forward to present day however, and we find the current members of GUN (including Agent Topaz) taking in their own past agents for their fifty year old Crimes.
* Happens to several lower ranking soldiers on both sides of the Bloody Valentine War in ''GundamSEED'', after the full scale of their superiors' [[FinalSolution genocidal intentions]] are revealed.
* [[spoiler:The Warriors]] in ''BurnUp Scramble'', though it shouldn't be too shocking, given it's run by an OmniscientCouncilOfVagueness. [[spoiler: Their own Commander]] ends up being the final boss, and the unit is disbanded in the aftermath of the final battle. However, it gets reinstated under new management in the end after [[spoiler:the girls show that the Warriors do in fact fight for justice]].

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[[folder: Film ]]

%%* The Fraternity in ''Film/{{Wanted}}''.

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[[folder: Literature ]]

* [[spoiler: President Coin's District Thirteen]] in ''Literature/TheHungerGames''.

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[[folder: Live Action Television ]]

* Happened in ''Series/BuffyTheVampireSlayer'' in Season 4 with Riley and the Initiative. Riley was a loyal soldier for the organisation and attempted to recruit Buffy as well, but eventually learned that the Initiative was using {{Mad Scientist}}s (particularly Walsh), [[SuperSoldier boosting its soldiers' performances]] with [[GovernmentDrugEnforcement drugs]] and [[HollywoodCyborg cybernetic implants]], and creating a cyborg SuperSoldier using [[NinjaPirateZombieRobot demon body tissue]]. After Walsh tries to kill Buffy, and the Initiative captures and experiments on Oz, Riley deserts and joins the Scoobies. After the demise of the Initiative Riley is [[PutOnABus headhunted by a military demon-killing unit]] that's less morally ambiguous.
** More subtly happened with the Watcher Council. After being increasingly shown to be doddering old men trapped in their old traditions unable to keep up with the changing of the times, in season 7 Buffy finds herself making many of the same decisions that the Council would have made.
* SD-6 from ''Series/{{Alias}}'' plays this card with its very first episode: a criminal organization masquerading as a black-ops unit of the CIA, wherein several of its recruits (Sydney, Dixon, and Marshall) are unaware of its true nature, and who are allowed to join the CIA once SD-6 is taken down. Granted, to many outside the USA, CIA Black Ops '''are''' bad, but SD-6 [[EvilerThanThou is even worse.]]
* [[InvertedTrope Inverted]] in ''Series/{{Millennium}}'', where the Millennium Group initially helps police with criminal threats, expanding to supernatural villains in season 2. Then in the second SeasonFinale they release a souped up virus that [[spoiler: kills Catherine Black]].
* In the ''HouseOfTheNight'' series, [[spoiler: Neferet is eventually revealed to be evil and using the school for her own ends.]]
* in ''Series/TheInvisibleMan'', despite the fact that Darien really doesn't like [[DaChief the Official]] or [[CovertGroupWithMundaneFront the Agency]], they don't really do anything ''that'' morally questionable (except keep Darien himself on a leash with the counter-agent; but he's an ex-con, so it may be justified). However, one episode has another government official get the Official arrested for a botched mission in which a hostage was killed and gets himself put in charge of the Agency and Darien. At first, things seem unchanged, but then the new boss tries to force Darien to become an assassin in exchange for the counter-agent (something the Official has ''never'' asked). Naturally, StatusQuoIsGod, and the Official is returned at the end of the episode.

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[[folder: Tabletop Games ]]

* In ''TabletopGame/BattleTech'', Precentor Martial [[TheAtoner Focht]] of [=ComStar=] tried to do this with the rather secretive and cult-like organization he belonged to. However, unlike most versions, [=ComStar=] ultimately wound up breaking down into violently opposed factions that used nukes to voice opposition.

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[[folder: Video Games ]]

* UNATCO in ''VideoGame/DeusEx'' follows this trope to a tee. JC Denton is recruited in from the start of the game under the impression he is stopping terrorists from stealing Ambrosia, a medicine for a wide spread virus. It turns out that the government is purposefully spreading the virus for their own agenda, and are withholding the cure for those who follow them, leaving the rest to die. The supposed terrorists are simply trying to spread the cure. JC is later captured and [[CardboardPrison he escapes]], and all his old friends join him if you talk to them on your way out.
* Gabriel Logan from ''SyphonFilter'' ends up killing half the top brass of the Agency, witnesses the deaths of the other half, and becomes the new head honcho, giving him authority to reform it into the more benign International Presidential Consulting Agency.
* Happens to Balamb Garden in ''FinalFantasyVIII''. Well, when your higher-ups are trying to sell you to ObviouslyEvil Sorceress Edea to save their own arses after a failed assassination attempt against her, it's only right that you kick their sorry butts.
* In ''DawnOfWar 2: Chaos Rising'', it turns out the Blood Ravens' Chapter Master and Chief Librarian is tainted, and has spread his rot through much of the chapter. Third and fourth companies, who are untainted, officially rebel against him in the expansion pack's ending -- depending on the party's purity level, this can be with the player's squad as the rebellion's most fervent supporters, or as another enemy for them to defeat.
* In ''TacticsOgre'', [[LaResistance the Walsta Liberation Army]] that recruits you in the beginning engages in a lot of morally questionable deeds, including massacring civilians to put the blame on Gargastan, which leads the Army to split into factions after the first chapter. If you stay with them and take orders (the Lawful route), then when [[spoiler: Leonard kills Duke Ronway and tries to kill you, you defeat him, use him as a scapegoat for all of the Walsta Liberation Army's crimes, and unite the Walsta Liberation Army and Neo Walsta Liberation Army into a single mostly-good resistance force.]]

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[[folder: Web Comics ]]

* This happens to Riff, the MadScientist from ''SluggyFreelance'' when Hereti Corp is revealed to be "the evilest corporation on Earth." [[spoiler:He responds by handing in his resignation... and blowing most of Hereti Corp up on his way out.]]

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[[folder: Web Original ]]

* In ''Literature/{{Worm}}'', this is in the process of happening to the [[SuperTeam Protectorate]], with the removal of [[WellIntentionedExtremist the Triumvirate]] and the purging of [[NebulousEvilOrganization Cauldron's]] influence. However, many of the superheroes that were alienated by the [[IDidWhatIHadToDo revelation]] of the Protectorate's crimes remain wary and independent.

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