The fanatic but charismatic Jet, a guerrilla freedom fighter from mid-Season 1, who reappeared near the end of Season 2 with the intention of redeeming himself only to discover that Redemption Equals Death.
General Fong: He continuously pressures Aang to forgo the elements he has yet to learn and go into the Avatar state so they can take out the firelord, not knowing the implications of doing so (as did the cast and audience at that point). He points out all the soldiers in the infirmary, and mentions the many that have died. He even starts attacking Aang with his soldiers, so they can release the state. He also buries Katara alive though not killing her because he doesn't want Aang to turn on him.
Sozin started off as this, but as he became older, he became more obsessed with power. It took until the end of his life for him to acknowledge this, and by then it was too late to change the course he had set, as his descendants dropped the "well-intentioned" part completely.
Hama. She wants to help fight the war so she does. By imprisoning innocent Fire Nation civilians.
Katara ALMOST became this, seeking revenge after a Fire Nation soldier who killed her mother. She was driven to such rage that she casually uses blood bending to find the man. Only at the very last second does she hold herself back from actually killing him.
The Equalists, who want non-benders to be treated fairly. It's just that their means to achieve this is by the removal of bending from the world.
Tarrlok, one of the leaders of Republic City, seems to be this as well. He wants to stop the Equalist threat, but he treats all non-benders as Equalists and wants to remove their rights. Subverted as he's really just trying to gain more power over the city and take it over like his father, Yakone, attempted to do before.
Korra's uncle, ChiefUnalaq of the Northern Water Tribe, with his suspect cheekbones and religious fervor, appears poised to be treated as one as well. Though he aims to restore spiritual harmony in his southern sister tribe and by extension the world, he appears willing to impose an occupational crusade upon them as a means of not-so-subtle coercion to get them back in touch with their spiritual sides.
This interpretation loses some of its credibility in episode 4 when it becomes known that Unalaq engineered the barbarian raid on the Northern Tribe that led to his brother's banishment. Korra claims he's power-hungry, envious of his brother's position as both the older brother who would have become chief, and as the father of the Avatar (and Chief in the Southern Tribe). However, there's no evidence that he's not still right about the Dark Spirits.
Eventually, it's established that he does believe in his rhetoric, and wants to bring balance to the world. Pity he hopes to accomplish this by fusing with the spirit of darkness and chaos...
This is discussed in Season 4 when Toph points out that all the villains Korra's fought had good ideas, and may even have had the best intentions at the start, but just went too far in their execution. This discussion is a major factor in helping Korra snap out of her Heroic B.S.O.D..
In the final episodes of Season Five of Star Wars: The Clone Wars, Barriss Offee becomes one by bombing the Jedi Temple, because she believed the Jedi Order was degenerating from peace-keepers into warmongers, and believed they should be punished for it. That doesn't justify a bombing that killed many innocent people, however. Nor does it justify framing Ahsoka to cover your tracks.
Equinox wants to balance Chaos and Order BY DESTROYING AND RESETTING THE UNIVERSE.
Kr'ull the Eternal simply wants to have an empire that won't age and die while he has to watch it suffer. He plans to replace all the humans in the world with eternal bodybuilders just like him. By the 25th century, he seems to have gotten over it.
Sideshow Bob: Because you need me, Springfield. Your guilty conscience may force you to vote Democratic, but deep down inside you secretly long for a cold-hearted Republican to lower taxes, brutalize criminals, and rule you like a king. That's why I did this: to protect you from yourselves.
On the other hand the first thing Bob did as Mayor of Springfield, was to bulldoze the Simpsons house.
Similarly, the episode "Sideshow Bob's Last Gleaming". Certainly, Bob claimed that he was doing a good deed by ridding Springfield of TV, but all it really did was make him the top dog in the manger.
Also, when Bob sees Springfield give into his demands, he exclaims "I should have made more demands!"
Bob's not the only one to utilize this trope: Jimbo Jones often steals dolls because he believes that they would harm girls. Even Bart Simpson has had shades of this. One particular example had Bart gaining increased intelligence from a drug, but then seemingly growing insane and beginning to believe that the MLB was spying on the town. He then went as far hijacking a tank from a military base, driving it across Springfield, and stopping in front of Springfield Elementary, and then proceeding to fire into the sky (after several tense moments where Bart periodically stopped the cannon on various locations [specifically, Springfield Elementary, The First Church of Springfield, and the Frame Shop, respectively]), shooting down the satellite, all in order to prove that he was indeed telling the truth and was certainly not crazy (well, for the most part).
Homer also had shades of this. One notable instance of this is when he decided to go all The Grinch on people on Christmas and steal gifts, because he legitimately believed that doing so would result in people actually caring for each other rather than focusing on themselves. Unfortunately for him, it backfired, resulting in the town hating him afterwards.
Marge exhibits at least one moment of this when she rallies to have all sweets banned from Springfield under "Marge's Law", leading to a bootlegging operation in which Homer himself is involved.
Mayor Quimby, the town's resident Corrupt Politician, also showcased shades of this. In one episode, he declared a 75 cent tax on the highway, and after people started evading it, tried to force people to go through the checkpoint. Why? Because he needed the tax money so that he could de-python the town fountain (which, as the phrase implies, means that the town fountain somehow got pythons in it, causing a panic when it sprays snakes instead of water, causing the occupants to leave). Another instance was when he tried to prohibit alcohol on St. Patrick's Day to reduce the potential amount of riots that would occur from being drunk, but it backfired when Irish Catholics and Irish Protestants were unable to put aside their differences without alcohol, and resulted in them still getting into a riot anyway.
Mr. Burns also sometimes has this as his motivation for some of his bad actions in some episodes: a particularly notable example was when he tried to ruin the Power Plant's union in "Last Exit to Springfield". The reason he felt that he should eliminate them was because he realized that it was becoming inherently corrupt, remembering what a worker his grandfather had dragged off had said, and wanted to destroy said corruption one way or another.
The Earl of Lemongrab fits this trope. Although he's a mean, sour, bitter, nasty-tempered Jerkass Woobie, his intentions are pretty good. All he wants to do during his reign of the Candy Kingdom is live in a place that's quite and clean, free of pranks, trouble-makers, and anybody who bothers him. But he tries to achieve this mild goal through the worst, most extreme methods- screaming constantly and sending everybody in the Candy Kingdom to the dungeon for ONE MILLION YEARS!!!
Princess Bubblegum fits this trope in the episode "What Have I Done". She wishes to cure the Candy Kingdom of their freezer-burn flu, by making the Ice King howl in pain. When the Ice King refuses, she resorts to making Finn and Jake capture him so she can beat the howls out of him. She later learns that it is not in Finn or Jake's heroic nature to beat people for no reason, and apologizes for forcing them.
Finn fits this trope a good deal of the time! If you've got a charismatic teenage boy who has super-strength and super-bravery, then odds are he'll probably use more than a few extreme methods during his zealous quest to conquer evil.
The Ice King. He just wants to have friends and a wife, when you really think about it. All of the awful things he does stem from his desire for companionship.
Agent Bishop from the second Teenage Mutant Ninja Turtles animated series has one mission: to protect Earth from an alien invasion. In order to achieve this, he has used aliens as unwilling test subjects for genetics experiments, faked an alien invasion and kidnapped the President in a ploy to guarantee funding for his agency, the Earth Protection Force, attempted to produce a sleeper army of super-soldiers to covertly kill people suspected of being aliens, and, ironically, prolonged an alien invasion in order to fulfill the terms of an agreement with yet another group of aliens. Eventually, however, deciding that diplomacy is a more long-lasting and effective way of protecting Earth, he gives up Black Ops.
In almost all incarnations of Transformers, Megatron is forced to become one of these because Decepticons were second-class citizens due to an earlier war. That is, of course, his only redeeming quality and it isn't a very good one.
Well, some of them are nice guys to those troops that don't betray them, and name Prime a "worthy opponent".
And note that, despite being "the bad guys", not all Decepticons are inherently evil. Many of them are just soldiers doing their jobs, and it's hardly their fault that the side they picked happened to have attracted the most psychos.
In Beast Machines, Megatron has a seemingly good idea, in principle. He wants to eliminate political squabbling, which results in nothing ever getting done, by uniting all machines under one mind. Of course, there are problems with this - Megatron is egomaniacal, wanting his mind to be the one in charge, sacrificing the minds of others and destroying those who would stand in his way (the Maximals). Also, he wants a purely technological world, eliminating all organic races (though aside from the Maximals, that already happened on Cybertron).
Nerissa, the main villain from W.I.T.C.H., used to be one of the good guys in charge of protecting the universe, but soon realized that the only way to truly protect the universe was to bring it under her rule, so that she could ensure that there would be no war, suffering, or injustice. For the most part, she ensured that no innocent people were harmed in her crusade, aside from the heroes who opposed her.
Not that she cares if innocent people get hurt, mind you. Considering how she treated her own minions (that she created, one of which was a copy of her successor that she killed after she refused to fight the original to the death, basically her children and created an actual son strictly to use in her plans. It's also implied that she was behind the first season's Big Bad rise to power as a part of an Evil Plan to obtain enough power to begin her conquest which lead to civil war on Meridian for over a decade. Her ideal world inside her prison at the end of Season 2 is one where everyone loves and obeys her, possibly meaning her "perfect world" mission statement is a self-delusion to cope with her It's All About Me tendencies. Also, her Start of Darkness was when she killed (accidentally, but still a serious loss of control) her friend after their boss gave her position to said friend. She was also petty enough to sic an animated garbage can on a vagrant just for looking at her wrong. This is not a person you want running your universe.
Ĉon Flux's nemesis Trevor Goodchild honestly believes that by walling off his entire country, placing surveillance cameras everywhere, and conducting bizarre experiments in psychology and genetics, he's providing an unobjectionably safe existence for his subjects and gradually improving their quality of life. The frightening thing about this show is that, half the time, you suspect he may beright... Aeon herself is generally determined to liberate people from order whether they want it or not and regardless of whether they survive, although there is one occasion when she decides a would-be refugee isn't really suited to live without organization and dumps him right back.
Examples of this trope often turned up as villains/antagonists on Super Friends.
Including one villain who thought that it was such a CRIME to spend money on space exploration instead of helping the poor...as opposed to shrinking a whole space center and kidnapping everyone inside?
Word of God claims that this is the way the Brain from Pinky and the Brain should be viewed. He wants to rule the world not for the sake of being a dictator, like his rival Snowball, but because he believes that he could do a much better job of it than the people currently in charge. (And Brain has, indeed, done everything in his power to prevent Snowball's evil schemes, knowing that a world under Snowball's rule would be the worst scenario.)
As seen in "Phineas and Ferbs Quantum Boogaloo" , as a result of Candace busting Phineas and Ferb for their rollercoaster, Moral Guardians embark on a misguided crusade for the abolition of creativity in children, ultimately having children be stored in People Jars until adulthood. All for the sake of keeping children safe.
Charlie Dog from Looney Tunes. Poor guy, all he wants is to be loved but he goes at it so wrong...
Ramses the Pharaoh from The Prince of Egypt. Rather than making him a cardboard cut-out villain, the creators wrote him as a "Well Done, Son!" Guy with a Freudian Excuse who has a very close relationship with Moses (they grew up together as brothers), who's just doing what he feels is right for the country and his dynasty. His father is the same, and even gives a little speech about how it is necessary to make sacrifices for the greater good (the "sacrifice" being the mass-murder of children). Of course, neither of them feel particularly guilty about ordering the massacre of slaves.
Ra's Al Ghul, who barely manages to scrape into the "well-intentioned" category. His rather vaguely-defined motive is to restore the Earth to its original, "pristine" state. His method is wiping out half of humanity.
Mister Freeze is introduced as one of the "revenge at any cost" variety, out to avenge himself on the Corrupt Corporate Executive who pulled the plug on the research he hoped to use to save his wife's life and caused the resulting Freak Lab Accident that made him what he is. Batman manages to stop him, and also finds evidence of the executive's own crimes to ensure he's brought to justice as well.
Justice League has the Justice Lords, an Alternate Universe counterpart of the League who crossed the Moral Event Horizon after Lord!Superman killed Luthor. Their actions in League's mainstream universe added fuel to the paranoia of other Well Intentioned Extremists, resulting in the foundation of Project Cadmus specifically to contain the Justice League, led by : Amanda Waller, Emil Hamilton and Wade Eiling.
When it comes to Project Cadmus, they actually come off as a weird inversion of Strawman Has a Point: though they genuinely do have a point in that it's reasonable to fear the League going rogue, as several of the League's own members (most notable the Badass NormalsBatman and Green Arrow) admit, the lengths they go to make them appear far more villainous than the League ever does, with a list of crimes that includes:
Taking metahuman children from their homes to rear them as Super Soldiers.
Cloning Supergirl and rearing her as a living weapon, including dispatching her to murder people on their say-so (Galataea).
Creating a mutated, deformed, clone of Superman and abusing him in order to render him a living anti-Superman weapon, then losing control of him (Doomsday).
Using a gang of super-criminals to break into the Watchtower's vault and make off with a mystical Weapon of Mass Destruction (The Annihilator).
Deliberately striving to discredit and aggravate Superman (Lexo City).
Engineering an entire team of genetically engineered "clone" superhumans and then replacing them with fresh clones when they invariably break down and die (the Ultimen)
One member, Wade Eiling, eventually goes so nuts he injects himself with Super Serum and outright attacks the Justice League in an effort to "prove" they are a threat.
Amanda Waller, meanwhile, eventually defects from Cadmus, but comes to admire Batman so much that she decides that his genes must continue, even if he himself seems determined to drive away every single potential love interest with his obsessive fixation on "the duty". She does this by genetically modifying an unknowing couple so the man's sperm is genetically Bruce Wayne's— something that's subtly implied causes their eventual divorce— and then trying to get an assassin to murder the parents of the resultant sons in the belief that the traumatic murder-by-criminals of both parents is an essential "ingredient" in the recipe for Batman. However, said assassin also happened to be Bruce's former love interest Andrea Beaumont, who is ultimately unable to go through with it because it would be going against everything Bruce ever stood for. Realizing she crossed a line, she abandoned the project, but as fate would have it, Terry McGinnis, the end result of her project, would go on to meet Bruce on his own, and lose his father to Derek Powers by chance, thus ensuring that the project was a success. Waller even admits to Terry that she knows she has a lot of sins to answer for with God when her time finally comes.
Magneto's depiction in the '90s X-Men cartoon also qualifies. When Xavier questions his ideas, Magneto states that attempting to go with reason against an enemy using force led to it getting crushed.
The Avengers: Earth's Mightiest Heroes! has Kang the Conqueror. The future where he comes from is being erased from existence, so he goes to the past to fix this. He decided that the best way to do this is to conquer the past to prepare the people of Earth for the coming Alien Invasion. And to add to that, he thinks that the future destruction is caused by Captain America. His solution? To kill Captain America in order to save his future. Too bad he went after the wrong one.
Dante's Inferno: An Animated Epic - Dante, before and during his time in the crusades. His unquestioning loyalty in his religious mission causes him to justify the beating of a prisoner for protecting a woman by claiming that he deserved what he got for being a heretic. He also uses his status as a soldier of god to gain comfort from the women whom the beaten prisoner was protecting, despite promising his wife that he would remain true to their marriage.
Soldier: "Dante, do not commit this wicked sin!" Dante: "How is it a sin, if I'm already absolved?"
The National Security Agency of The Zeta Project veer in and out of this trope. They exist to take down high tech terrorists and threats to human life, basically serving as the FBI and CIA of their universe. However, they themselves have had a lot of morally gray moments. Allowing a mad bomber to kill people because he'd get a terrorist they were after in the process, for instance, along with a lot of human rights violations all over the place. You have no right to a trial, they do not need a search warrant, they can detain you against your will, you do not have the right to an attorney when interrogated, and they carry weapons that are a lot more vicious and brutal than bullets. The zigzagging trope part comes in when they're proven to be completely right half the time and, as a part of the DCAU, they've faced end of the world scenarios before.
In the 1930s MGM cartoon "Jitterbug Follies", Count Screwloose tries to scam the public by selling tickets for a show that won't go on, but a group called "Citizens For Fair Play" tell him to put on a show or else. They happen to to act and dress like 30s-style thugs.
On Gargoyles,Demona has undergone so much pain over the centuries due to humans that she basically wants to wipe them out so that gargoyles can inherit the Earth.
On the other hand, she cannot admit to herself that a large part of the pain she suffers from is her own fault, blaming upon the humans her own mistakes.
While the villains of Captain Planet and the Planeteers are strawmen at best, Sly Sludge and Looten Plunder occasionally come off as this. Sly Sludge's plans normally result from carelessness while trying to dispose of waste. It's not a bad goal by any means... he just doesn't know any better.
Looten Plunder happens to come off as this during the episode "Bitter Waters". He approaches an Indian Reservation barely sustaining themselves with a proposition of setting up a business there. It provides the people of the reservation with paying jobs and money to spend, but causes environmental damage when Selenium starts tainting the water and he starts wasting it. For once, he doesn't get away because this was on an Indian reservation, and at the end of the episode when the people set up wind turbines and grow crops native to the area, admits they didn't need him after all, while working in the fields as punishment.
Kaia and the Terras in Motorcity, they oppose Kane like Mike Chilton and the Burners, as Kane spilled toxic waste into their home, mutating their environment and their bodies, but their plans to oppose Kane involve harming innocent Detroit Deluxe citizens.
The Mayor becomes one in the episode "Hot Air Buffoon." He wanted to fight crime without relying on the girls all the time, so he rides an air balloon with a boxing glove and starts punching out criminals...then he starts punching out innocent citizens in the process. The girls have no choice but to stop him.
Shockingly, Mojo Jojo turns out to be one. His hatred of the Girls is unquestionably wrong, but when it comes to taking over the world, he actually has its best interests at heart - the moment he takes over, he ends all its major problems. Once he accomplishes this, he's not even hostile toward the Girls anymore... until he gets bored, at least.
The Great Computer and his late creator, doctor Shibas, from the French animated series Il était une fois... l'Espace (Once Upon a Time... Space). Their objective is the welfare of all sentients and defense against any and all tyrants and dictators, but already when Shibas was still alive they were willing to use the overwhelming military power of the immense and well-equipped army of robots built on Yama to do so. They come close to be right, what with the general Pest being a mad dictator that Omega cannot deal with due his enormous military strength. Shibas never considering using military strength until the construction crew he had invited from the nearby Death World of Apis to build a city for their people destroyed one of his labs and factories, because he wasn't out there to help them personally instead of sending capable construction robots to do the job. They miss being right, though, due the horrible living conditions they force the human inhabitants of Yama and Apis (descendants of the construction crew and the colonists of Apis) into... And, knowing this, the Great Computer is trying to learn how to be a good ruler.
Stimpy in Ren and Stimpy's first cartoon acts like this - he wants Ren to be happy after his last invention, the Stay-Put Socks, pisses off Ren. So he builds the Happy Helmet, which forces him to be happy!
The original Superfriends was full of guys like this, who were trying to save humanity (or thought they were) or one group of people through their actions, without considering the consequences. One example was a scientist who thought shrinking people could solve world hunger. (Since shrunken human ate far less than normal-sized ones, it made sense, right?) Another example was a scientist who altered the Gulf Stream to the point where he could practically control the weather; his intent was to aid his poverty-stricken nation of Glacia with better farmland, even if it crippled the rest of the world, as he was sure nobody else cared about them. (In truth, nobody else had even heard of them, and simply asking for help could have avoided a lot of problems.) Another was an alien from Venus who was trying to make the environment of Earth more like his planet so his people could colonize it, because industrial pollution had made the temperature on Venus too cold for them to tolerate. (Again, simply asking for help never occurred to them.)
The Society of The Blind Eye, whose goal is to help people forget about their bad memories, and to keep them happy and ignorant of the supernatural happenings in Gravity Falls. Unfortunately the memory ray slowly destroys the mind of its target with repeated use, and it most likely caused the stupidity of the townsfolk.
The author, who turns out to be Stan's brother may have been one, hoping to create a device that benefited mankind, but caused a terrible accident, so bad that McGucket, who was his assistant, created the memory gun just to forget about it.
Stan himself spent thirty years trying to rebuild the portal and bring his brother back. But he committed a lot of crimes, from false identification to theft of toxic waste, to rebuild it. Not to mention lying to his family, and ignoring the warning that activating the device could have triggered The End of the World as We Know It.
The Season 5 finale later reveals that Starlight Glimmer adopted her ideology of friendship through total equality because her childhood friend, Sunburst, left her when she was a filly after receiving his cutie mark. This caused her to blame Cutie Marks for what happened, and to create her equality village, in hopes of creating a society where nopony could boast about being different or being better than others, and on top of all that, nopony would leave anypony else just to follow whatever destiny their Cutie Mark represents, like how Sunburst left Starlight.
Rick and Morty: Unity wants to bring peace to the Universe by turning all life into a single Hive Mind without any individuality.
Steven Universe: After Steven accidentally un-bubbles the gem in Lion's mane, we meet Bismuth, who was one of the original Crystal Gems. In the final act of that same episode, we discover that she was bubbled by Rose Quartz for developing a weapon that could easily shatter a Gem's gemstone instead of just destroying their physical form (as long as the gemstone is intact, their species can regenerate the body in a matter of minutes). Such a tactic, while it would have likely helped win the Great Offscreen War with less causalities on the Crystal Gem side, was deemed as stooping to Homeworld's level by Rose. This sentiment is shared by Steven, which leads to Bismuth beind bubbled once again and the weapon destroyed.