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.

Examples of Conspiracy Redemption include:

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 assassinated and secretly replaced 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 a Chessmaster used a perfectly legal means to kill Rukia and the Captains were just doing their jobs. Ichigo was invading a city-state to rescue a criminal.
- 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 - 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 could 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. 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. 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 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. 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 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. I guess this is a case of them not being responsible for the crimes of their predecessors.
E's Otherwise

Film

The Fraternity in Wanted.

Literature

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.
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, Neferet is eventually revealed to be evil and using the school for her own ends.

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 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.
In Honkai Impact 3rd it is eventually revealed that Schicksal's Overseer Otto Apocalypse is the one responsible for the return of the Herrscher of the Void and all the harm resulting from that. This leads to St. Freya breaking off to join with Anti-Entropy in battling him.

Web Comics

This happens to Riff, the Mad Scientist from Sluggy Freelance when Hereti Corp is revealed to be "the evilest corporation on Earth." He responds by handing in his resignation... and blowing most of Hereti Corp up on his way out.