Conspiracy Redemption

Frequently, a Hero, (especially an Ordinary High School Student) 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 The Hero gets to hang out and bash monsters with their new best pals (bonus points for alienating their usual group of friends in the process), several hints and a few subplots will start to appear that cast the intentions of "The Organization" into doubt. They will attempt to coerce the hero into doing morally questionable things (maybe discrediting him or branding him a heretic, inappropriate use of force, or threatening to take away his powers), and they will be doing some other evil deeds that betray the mission or ethics the company once proudly touted as "elevating it" above mere 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 organization as a whole are not really evil, there are only a few corrupt members (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 Good All Along, Villain with Good Publicity.

Anime and Manga

 * This becomes the entire second Arc of Bleach once the Ordinary High School Student protagonists, the setting and basic premise are established. The entirety of Soul Society's Executive branch is out to kill the heroes: lower officer Rukia, because her emergency illegal act was declared an executable offense by the  Congress, and kill the heroes for trying to rescue her from being executed. The kicker is, after this minor misunderstanding is cleared up, Rukia goes right back to work for the people that were willing to kill her and Ichigo becomes an honorary substitute officer. Yay! They got sheriff buttons! The only justifiable bit is that
 * Also, the Soul Society was divided over Rukia's execution. Her Captain was one of the ones who revolted against the other Soul Reapers, and he helped Ichigo rescue her. So it's no surprise they'd still be willing to work for the guy.
 * The Law of Ueki
 * Busou Renkin, though without any actual evil or corruption going on -
 * 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. I'm really not kidding. No, seriously. Even use of anaesthetic puts you on 'the good guys' side.
 * 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.
 * 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).
 * 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  In both the manga and the anime adaptation, 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
 * 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.
 * 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. I guess this is a case of them not being responsible for the crimes of their predecessors.
 * E's Otherwise
 * E's Otherwise

Film

 * The Fraternity in Wanted.

Literature

 * 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.
 * 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.
 * Millennium.
 * In the House of the Night series,

Tabletop Games

 * In BattleTech, Precentor Martial Focht of ComStar tried to do this with the rather secretive and cult-like organization he belonged to. However, unlike most versions, infighting very much occurred. And by "infighting" I mean "nukes. Lots and lots of nukes". Though not right away.

Video Games

 * 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

Web Comics

 * This happens to Riff, the Mad Scientist from Sluggy Freelance when Hereti Corp is revealed to be "the evilest corporation on Earth."