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Anime and Manga
- In Digimon Tamers, 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 Bleach once the Ordinary High-School Student protagonists, the setting and basic premise are established. The full brunt of Soul Society's Celestial Bureaucracy is brought to bear against the heroes: lower officer Rukia because her emergency illegal act was declared an executable offense by the assassinated and secretly replaced Central 46, and the human kids because they try to protect Rukia from arrest and execution. Several members of the Soul Society hierarchy join forces with the main cast, some due to considering Rukia's sentence unjust and some for more personal reasons, promptly gaining roles as secondary protagonists in the process.
- The Law of Ueki
- Busou Renkin, though without any actual evil or corruption going on - the Alchemist Army tries to kill Kazuki because he will eventually become, after six weeks, a tremendous threat to everyone around him.
- 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.
- Elemental Gelade
- Deadman Wonderland
- 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.
- Chronos in Black Cat.
- Witch Hunter Robin 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). 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 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.
- Martian Successor Nadesico, 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 Neon Genesis Evangelion, 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 Fullmetal Alchemist, we eventually learn that the entire state military is in fact a tool for the evil Homunculi, one of whom is in fact the head of the military. Though really, he is called the Führer. Idealistic members try to stop them from succeeding.
- A somewhat darker variant appears in Darker Than Black — The Syndicate 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 to have an agenda involving exterminating the contractors as a whole by closing Hell's Gate (Evening Primrose beat them to Heaven's Gate). Both Hei, his True Companions, and November 11 become examples of this trope when they find out, and in the latter cases Conspiracy Redemption Equals Death.
- 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 controlled by the UN, as are most of the supposedly opposing groups.
- In the Sonic X 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 Mobile Suit Gundam SEED, after the full scale of their superiors' genocidal intentions are revealed.
- Shinn Asuka from the sequel series is an aversion, and possible deconstruction, of this trope. His mess of anger issues keeps him from seeing anything but shades of black and white, and the resident Chessmaster and his Dragon exploit this. Shinn remains blind to their manipulations for almost the entire series, convinced that he's on some sort or righteous, world-changing crusade even when he's participating in missions that go against everything he claimed to stand fornote . To his credit, he starts having doubts near the end of the series, but by then he's become so reliant on their advice that this just makes him more deranged. He does realize what's going on at the very end, but it takes a pretty nasty beating from Athrun and the Infinite Justice to get to that point, leaving him unable to do anything except watch as the whole scheme goes up in flames.
- The Warriors in Burn Up Scramble, though it shouldn't be too shocking, given it's run by an Omniscient Council of Vagueness. 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 the girls show that the Warriors do in fact fight for justice.
- President Coin's District Thirteen in The Hunger Games.
Live Action Television
- Happened in Buffy the Vampire Slayer 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 Scientists (particularly Walsh), boosting its soldiers' performances with drugs and cybernetic implants, and creating a cyborg Super Soldier using 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 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 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 is even worse.
- Inverted in Millennium, where the Millennium Group initially helps police with criminal threats, expanding to supernatural villains in season 2. Then in the second Season Finale they release a souped up virus that kills Catherine Black.
- In The Invisible Man, despite the fact that Darien really doesn't like the Official or 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, Status Quo Is God, and the Official is returned at the end of the episode.
- The Department of Extranormal Operations in Supergirl was originally founded and run by xenophobes who were terrified of Superman and were willing to abduct Kara when she was a girl. After J'onn J'onzz secretly replaced Hank Henshaw, he began slowly refocusing the organization on actual threats instead of innocent aliens.
- Torchwood is an entire series dedicated to this, where Captain Jack Harkness reforms the remnants of the titular shadowy anti-alien organization into a more benevolent force protecting Earth from alien threats.
- The Immortal angle in TNA revolved around Hulk Hogan and Eric Bischoff's secret plan to take over pro wrestling, starting with TNA, as to be expected. Part of this involved absorbing Ric Flair's Four Horseman successor group, Fourtune, but while Ric was away, Fourtune rebelled due to Bischoff mistreating them (especially AJ Styles) and Fourtune had basically been baby faces the entire time anyway given their entire motivation was stopping invaders of TNA.
- In BattleTech, Precentor Martial Focht of ComStar tried to do this with the secretive, quasi-religious organization. However, unlike most versions, ComStar ultimately split into two violently opposed factions (Comstar and the Word of Blake) and their disagreement eventually erupted into a massive war that engulfed the entire Inner Sphere.
- UNATCO in Deus Ex 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 he escapes, and all his old friends join him if you talk to them on your way out.
- Gabriel Logan from Syphon Filter 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 Final Fantasy VIII. Well, when your higher-ups are trying to sell you to Obviously Evil 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 Dawn of War 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 Tactics Ogre, 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 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.