Brainwashing for the Greater Good

So, the heroes have finally captured Duke Diabolico, yay! ... so now what? He's repeatedly proven he not only doesn't want to reform, but will turn any such attempts into another dastardly scheme by masquerading as reformed, and the Cardboard Prison is looking especially porous right now. Plus, he's proven smart enough to defy being a Self-Disposing Villain and even if the heroes weren't too principled to kill, he's also avoided giving the heroes (and other villains) reasons to kill him.

There's only one thing to do. Brainwashing... for the greater good! This can be done with varying degrees of squick. Heroes might go the "soft" route and administer Care Bear Stares, use The Power of Love and Friendship, and in conjunction with "motivational" speeches trigger a quasi-voluntary Heel Face Turn. However, a more extreme villain might require a more extreme method. The combination of Laser Guided Amnesia, a new personality, and a Restraining Bolt might be in order.

Who cares about Mind Over Manners if Duke Diabolico is no longer a threat and is helping old ladies cross the street? He might even join the heroes and help capture and brainwash other villains! But why stop there? Why not paint smiles on everyone's soul? Eventually, the heroes will be dumped at the bottom of the slippery slope: a world of Grey and Gray Morality where the horrific after-effects manifest.

If Duke Diabolico doesn't spontaneously relapse and kill willy nilly in reprisal for being demeaned into planting posies in the park, his minions or allies will come by and break the brainwashing. When this happens, it might even turn out that he likes good more than evil. If so, it will cause a Heroic BSOD as he grapples with a hidden lifetime of evil. Of course, it might be that the brainwashing had the side effect of turning him Brainwashed and Crazy.

What the hell, hero?

Compare Heel Face Brainwashing, and also see No Medication for Me for a trope that touches on the same ethical questions.

Anime and Manga

 * This is Tobi's main goal in Naruto. He plans to cast a permanent genjutsu on the moon that will make everyone live without hatred, since he believes mankind cannot live in such a way of their own free will.
 * Possibly. It's just as likely that he's lying about doing it for anyone else's benefit, and that all he cares about is dominating everyone.
 * In the world of Neon Genesis Evangelion, it is possible to brainwash EVA pilots into fighting, but this is never actually used (presumably the results would not be pretty).

Comic Books

 * Superman's Elseworlds counterpart in Red Son did this, to disturbing effect.
 * Doc Savage used to use psychosurgery on his enemies to remove criminal tendencies. Hey, If it works, it works!
 * In the Exiles comic, at the end of the "World Tour" story arc, Proteus (who had taken over the body of Morph) was brainwashed into thinking he really was Morph.
 * Used on Dr. Light in The DCU. It opened a floodgate of crap.
 * Attempted on Magneto in his many Marvel Universe incarnations. However, due to Personality Powers and Joker Immunity, he reverted to his original mindset
 * World's Finest #148, Superman and Batman—Outlaws! Our heroes suggest to the good Alternate Universe Lex Luthor that he should brainwash their evil counterparts into becoming good guys. This apparently works, but the brainwashed people are seen only from behind, so one could imagine that their faces told a different story.
 * In Green Lantern, the Star Sapphires will brainwash members of other Corps that they capture to turn them into servants of Love. While not exactly good-guys, the Sapphires are far from evil and this is easily the most questionable thing they've ever done.
 * In the original run of Marvel's Squadron Supreme, brainwashing villains and other criminals into becoming law-abiding citizens became part of their Utopian project. Unfortunately, this caused a rift in the group, and some of the rebelling heroes joined with villains, one of whom discovered how to reverse the process.
 * One Flash Gordon story centered on a tank-sized ray that could turn entire crowds into happy, good-hearted pacifists. Ming the Merciless takes control of it and use it to subjugate the opposition, until the protagonists manage to turn it on him. Flash even remarks what a swell guy Ming is when he's not evil. Justified since the ray's effect is temporary, and the rebound causes a lot of trouble later on.
 * Doctor Strange on occasion has used Laser Guided Amnesia to make villains forget the evil magic they have learned -- mostly for those who stumbled into it by accident and had no idea what they were doing.

Film

 * The use of the eponymous ark in the Stargate SG 1 movie The Ark of Truth to convince the Ori's followers of the error of their ways could be viewed this way. While it is justified in that A) the Ori are dead anyway, B) the Ark can only make people believe what is true, and C) the Ori's followers are on the verge of overrunning the Milky Way, it's still brainwashing. Even Daniel, who found the ark and figure out how to activate it in the first place, isn't happy that they had to use it since it does mess with free will in a disturbing way.
 * It's only programmed to brainwash the truth. While the Ark itself is hardwired to never be used for anything else, the technology could be adapted to make anyone believe anything. There's a reason the Ancients didn't use it in the first place.
 * Doc Savage: The Man of Bronze. At the end Doc performs one of his personality-altering operations on Captain Seas, who ends up as a member of the Salvation Army.
 * Deconstructed in the film and book A Clockwork Orange.
 * Drop Squad. A group of black Americans kidnaps and deprograms (brainwashes) blacks who act like white people. The intent is to restore their pride in their own race (DROP stands for Deprogramming and Restoration of Pride). The movie justifies this by having the black man who's kidnapped working for a company that acts in an outrageously racist manner that would never be accepted in Real Life. Other kidnap victims include a corrupt politician and a drug dealer.

Literature

 * The Stainless Steel Rat.
 * It works, though. Angelina turned from a murderous psychopath into a loving wife and mother... with occasional psychopathic tendencies, especially if you so much as look at her twins wrong.
 * In The Emerald City of Oz, Ozma decides this is a morally acceptable way to subdue invaders.
 * The wizard Mizzamir invented a spell to do this in Villains By Necessity. The villains are utterly horrified at the implications.
 * In a noncanon Percy Jackson and The Olympians side story, Percy battles the Titan Iapetus near Lethe, the River of Forgetfulness. Percy dunks himself and Iapetus in the river. Percy, being a son of Poseidon stayed dry, and Iapetus is soaked so he forgets everything. He gets renamed Bob and even helps cure some nasty wounds.
 * It is canon, or close enough. The storis have already influenced the canon books. Percy mentions in 5th book that he's seen Persephone in winter (which happened in the same story with Iapetus/Bob), and in The Heroes of Olympus, the kids use the bronze dragon from one of the other stories as transportation for their quest.
 * The heroes of Captain Underpants do this to.
 * In the original Doc Savage magazine stories, Doc performed "a delicate brain operation" on criminals to cure their criminal tendencies. It also removed all memories of their criminal past.
 * This is a prime example of Values Dissonance. Back in the 1930s, it was believed that ongoing criminal behaviour was a result of malformation of the brain, essentially a medical problem.
 * The "demolishing" process in The Demolished Man might well qualify.
 * in The Dresden Files does this in an attempt to stop her friends from using drugs while one of them pregnant (without consent from either of them.) It does not end well, and she is nearly executed for practicing textbook black magic.
 * Confessors from the Sword of Truth work like this. Unfortunately, the recharge time is anywhere from hours to weeks, and there's usually a lot of angry soldiers between a Confessor and a big bad. This is part of why they usually had a wizard bodyguard. The Confessors were mostly used to get the confession of condemned criminals who were part of conspiracies, but refused to cooperate.
 * Resoundingly averted in Robert Heinlein's "If This Goes On". The revolutionaries, after overthrowing the Corrupt Church, vote to reject their psych experts' proprosal to use Subliminal Seduction to "condition" the people to accept the restoration of democracy (after an old man who "looked like Mark Twain" made an impassioned speech on how "free men aren't 'conditioned'.")
 * Resoundingly averted in Robert Heinlein's "If This Goes On". The revolutionaries, after overthrowing the Corrupt Church, vote to reject their psych experts' proprosal to use Subliminal Seduction to "condition" the people to accept the restoration of democracy (after an old man who "looked like Mark Twain" made an impassioned speech on how "free men aren't 'conditioned'.")

Live Action TV

 * Doctor Who, The Mind of Evil. The Keller Machine removed the impulse to commit evil acts by subjecting its victims to their worst fears. Sometimes those fears would kill the people the machine's inventors intended to cure, which anticipates A Nightmare On Elm Street as well as echoing A Clockwork Orange.
 * In Underworld, the Minyan "humane" weapon is essentially a (temporary) lobotomy gun. The Doctor,, actually praises them for this.
 * The Sarah Jane Adventures, when Mr. Smith is rebooted.
 * Sylar in Heroes had his mind replaced by that of Nathan Petrelli, the man he had just killed. Because he had a shapeshifting ability, Sylar actually became Nathan. It lasted about six episodes.
 * On Babylon 5, a machine is used to wipe away the memories from serial killers and other major criminals and give them a new personality that will encourage them to help the community they harmed. Telepaths do not carry out the process, but do scans before and after to confirm success.
 * In Farscape, the Nebari ruling body "The Establishment" could subtlety modify a person's mind until they no longer had any negative impulses. Unfortunately, along with things like sadism, they considered having any individual desires to be negative qualities, and would happily modify anyone they deemed necessary (aka. most of the known galaxy).
 * It also backfires horribly with Durka in "A Clockwork Nebari." And, of course, the Nebari themselves are unwilling to consider the possibility that the "mind cleansing" could be overcome and cause even greater problems.
 * In an episode of Star Trek Voyager, a ruthless amoral criminal was found to have a faulty brain connection in the part that creates guilt, which was easily repaired. After that, he felt total remorse for everything, but it wasn't enough to convince his planet's justice system to let him go scot-free.
 * May be justified, as his personality isn't changed, he just felt guilty about his actions, essentially curing him of sociopathy.
 * Another episode has a planet of psychics where having a violent thought it a crime. The punishment is "mental surgery" of sorts that removes the offending thoughts from the person. When the local policewoman finds out that Federation puts criminals in "cages", she is horrified. Then B'elanna Torres (a half-Klingon with a nasty temper) is arrested for having a violent thought and sentenced to the "surgery". Naturally, the crew is worried that there may not be a B'elanna left after all her violents thoughts are removed.
 * In Kamen Rider Decade, there's a world where everyone is super-polite, super-helpful, and perfectly happy.
 * A web series tie-in to Dollhouse shows that one of the scientists who worked on the precursor to Active technology used it to fix her emotionally unstable daughter.
 * In the show itself, it is stated that some of the earliest Actives were exceptionally violent criminals (such as the serial killer serving a life sentence who was Alpha's original personality) who were taken against their will with the intention of forcibly turning them into reformed citizens who could then be released back into society to help with prison overcrowding. Judging by Alpha's case, this plan doesn't seem to have worked very well.
 * It is also hinted that the technology could be used in this way for some positive applications, such as curing mental illnesses. For example, Sierra was taken against her will as a "charity case" because she had schizophrenia (the Dollhouse staff not knowing/believing that she had schizophrenia because a man she rejected was drugging her). Unfortunately, these are vastly overshadowed by the much more dangerous negative applications, most of which fall under some variation of Brainwashed and Crazy.
 * In Angel, Angel becomes the CEO of evil lawfirm Wolfram & Hart's L.A. branch in exchange for them altering reality to give his son Connor a well-adjusted past with a normal family, and wipe everyone else's memories.

Tabletop Games

 * The Tau in Warhammer 40000 are implied to brainwash other races for their literal Greater Good.
 * Implied, as in, Imperial scribes say they do. And The Empire is notoriously xenophobic. So there's no way to tell whether it's true or not. The only way to know for sure is to ask an Eldar farseer (who are rumored to have genetically engineered the Tau Ethereal caste - the alleged brainwashers) but Eldar being Eldar, they have no reason to tell the truth.
 * The Imperium is also known to do this. Since the galaxy is full of things that can permanently corrupt a man's soul just for looking at them, it occasionally occurs that someone you'd rather not 'save' (that is to say, summarily execute) ends up a wee bit mad. The Imperium sorts this out by brainwashing the subject and either putting in fake memories or leaving the person blank. This allows them to continue service without being a risk of heresy. The Inquisition uses this tactic more than other factions.
 * It's evil on evil, but Suthaze magically brainwashed an evil dragon into thinking he was a friendly duck named Willie. Snarf broke the spell temporarily to distract Suthaze, but it was rendered permanent by massive head trauma.
 * Dungeons & Dragons' third edition Book of Exalted Deeds contains the Sanctify the Wicked spell, which has this effect, not only changing an Evil character to Good, but also changing the victim's alignment to Law or Chaos to match the caster's.

Videogames

 * in Knights of the Old Republic
 * It is suggested in the sequel that . He just lost his memories and changed methods, but his motivations and goals never really changed. All he really did in the first game was clean up the mess he made by his backstabbing apprentice, then before the start of the second, he left to continue where he left off.
 * Seeing as, they only wiped the slate clean and hoped to carry out the overarching plan properly.
 * In the novel Revan, it's a plot point that doesn't actually remember being a Sith lord or meeting The Emperor on Dromund Kaas. After the Exile gives  back the Sith mask, it triggers a flood that returns all the memories. Additionally, it increases 's power Up to Eleven, allowing him to easily beat a powerful Sith lord. Unfortunately,.
 * Starcraft: Much of the Terran military is made up of 'resocialized' criminals. The training process of Ghosts involves this as well, though they aren't necessarily criminals; The program will take anyone with enough potential. One would hope this statistic doesn't apply to the higher command.
 * Interestingly, Nova (one of the most powerful, if not THE most powerful, Terran psychics ever) actually chose to have her memory wiped, unable to cope with the memory of.
 * In Megaman Battle Network 5,.
 * In 's loyalty mission in Mass Effect 2, the heroes find out a way to turn the  Geth against the Reapers by introducing a computer virus into their network, essentially overwriting their thoughts. Given that the 'verse features several villains (including the Reapers) and Well Intentioned Extremists trying or succeeding in doing the same for their less-than-noble purposes, the parallels are made quite clear.
 * Interestingly, this isn't treated like the obvious good option, with several characters pointing out that if you alter the geths' thoughts, you're still "killing" who they used to be. The alternative is to kill all those geth outright, but...it's still a strange moral issue.
 * makes the point that the Geth are not a race of individuals like most other races, but a Hive Mind collective of inter-networked A Is. To equate their concept of morality- and attitude to the "brainwashing" option- to that of humanity is racist.
 * In Xenosaga, criminal justice involves multiple levels "personality reconditioning." Albedo was sentenced to and underwent high level "personality reconditioning" twice--one that saw him stripped of human status and permanently assigned the status of a Realian--for two separate killing sprees.
 * In the Dragon Age universe, mages can be made 'Tranquil', robbing them of the chaotic influence of emotions and thus rendering them slavish, robotic, atonal and altogether compliant to The Greater Good.
 * Or for... less savory purposes. Really, how much the Rite of Tranquility falls under this trope depends on the morality of the people using it, and whether the mage in question was willing (or at least beyond saving) or not. The morality issue is brought up frequently, and the ritual remains extremely controversial, both in-universe and out.
 * Deconstructed in Strange Journey. When the Chaotic Evil members of Jack's Crew leave the Red Sprite with little choice outside of kill or be killed, Zelenin tries to Take a Third Option by appealing to the angel Mastema for help. He offers to turn her into an angel so her hymn can turn their hearts back to God. It worked extremely well.
 * Later, a demon refuses to let you anywhere near Mother Maya unless you slaughter Jack's Crew. Zelenin offers to use her song to brainwash the demons as well. The problem here is that if you accept the demon's terms, you're killing people who can't really fight back... but the demons are survivors of Jack's Crew's vicious experiments, so they're kind of in the right.
 * In the end, the fate of Jack Squad is only foreshadowing
 * The MK Guns are an earlier version of this. It's implied they were designed to force altered states of consciousness.
 * This is how criminal rehabilitation functions in Startopia. Apart from removing all current criminal impulses from the subject it appears to have no other side-effects and allows the ex-criminal to fully re-enter society (and re-offending is possible if the peep gets enough of a soul hit later), making it one of the less problematic instances of this trope. Besides, you get paid 1000e per rehabilitated subject.

Web Comics

 * The Legion in MSF High used to do this. A lot. Or, at least they saw it like that. Most people saw them as the 'Heels', at times, and Legion transformations can have this effect, if done unwillingly. One of the reasons people don't like them very much. Generally, they don't do it now, though.
 * Threatened in the forums, to this one guy, Dracon, by a Legion NPC. He HATES said NPC now, with a passion.

Web Original

 * Maven tries to hypnotize The Nostalgia Chick into never thinking about Todd in The Shadows again, but it doesn't even come close to working.

Western Animation

 * In Justice League Unlimited, the alternate universe Knight Templar Justice League, the Justice Lords, brainwashed dangerous villains like The Joker. Or rather, Superman lobotomized them with his heat vision. (When Doomsday - freaking Doomsday shows up, this makes for a Curb Stomp Battle with the Justice Lord Superman. Instead of fistfighting to their mutual destruction, brain-fry ensues and it's a done deal. Of course, .)
 * Amusingly, when we get to see the alternate Arkham Asylum and the various lobotomized supervillains, The Ventriloquist has no lobotomy scars, but Mr. Scarface does.
 * Subverted in one episode of Star Wars: The Clone Wars, where this strategy is used via Jedi Mind Tricks, but tortures the villain so much that he agrees to tell what he knows before the brainwashing actually does its work.
 * In Sherlock Holmes in the 22nd Century, criminals who are captured are all put in a machine that removes their desire to commit crimes. The series kicks off when a Mad Scientist finds a way to protect himself from this and starts committing crimes again, including cloning Professor Moriarty.
 * In one SpongeBob SquarePants episode, Spongebob and Patrick brainwash Man-Ray into not doing evil stuff anymore, by tickling him when he does.
 * The Teenage Mutant Ninja Turtles once somehow managed to get Shredder thinking he was Michaelangelo. Cue wrath when the spell is broken.
 * In Street Sharks, after the police capture Repteel, Dr. Paradigm says that if they hand him over, he'll brainwash him into being harmless. Of course, given that Repteel's one of his henchmen, this is just an excuse to get the mutant out of prison.