I was away for a few years and I came back to a world in ruins. Death, destruction, chaos, the endless fighting—it was like the Heterodyne Boys had never existed. Things were worse than ever. So I stopped it. And I did it my way this time. No more negotiating. No more promises. No more second chances. And I did it alone.Because I had to.
The basics are simple enough, revolving around getting everyone into the same crummy situation so that they can sympathise with one another, but between Charles already (unknowingly) doing that, resulting in Lelouch's United Federation of Nations (UFN), and the very short amount of time and lack of mingling done by those nations that Lelouch was terrorising, with some nations are implied to be under Lelouch's control for a matter of days or weeks, it's difficult to believe that Lelouch's gambit is capable of creating a lasting effect, rather than bouncing back into their old habits, or reinforcing the idea of Britannians being evil.
Most importantly, the bulk of this plan - the part after "steal nuclear weapons" - is put into action over a mere ten minutes of screen time. That's 1% of the total air time of Code Geass, and is overshadowed by more important events!
In the manga version of Death Note, Near acknowledges that Light did in fact reduce the world crime rate by 70% and bring an end to all wars, despite his... unorthodoxmethods of doing so.
Tengen Toppa Gurren Lagann: Lordgenome became the Spiral King and killed off most of humanity so the Anti-Spirals wouldn't return and wipe them out. It was working just fine until Simon came along. Not a pleasant state of affairs, but better than extinction.
In Tiger & Bunny, HERO TV was started during the early days of NEXT-empowered people, and suffered due to widespread anti-NEXT prejudice. Albert Maverick formed an alliance with the criminal organization Ouroboros, trading technology and resources in exchange for flashier crimes and incidents for the heroes to resolve. The end result was HERO TV becoming massively popular, lasting for over two decades, and the positive exposure of NEXT superheroes led to greater acceptance over time. When he is finally cornered in the last episode he also mentions that Sternbild city was a run-down dump until the sense of security the Heroes provided made it prosperous.
If the Freezing Alchemist Isaac MacDougal at the start of Fullmetal Alchemist: Brotherhood had succeeded, even if it didn't stop Father's plan, it may have at least neutralized Wrath.
Shakugan no Shana: Yuji Sakaimerges with the Snake of the Festival so that they can create a world where Crimson Denizens can live without consuming the Power of Existence of humans (thus killing them and erasing them from existence), thus saving numerous humans, and also ending the threat to the balance of the world, removing their point of contention with the Flame Haze, and finally ending the Forever War. Flame Haze, especially Yuji's love interest Shana, will be able to be more than just tools and walking weapons, but actual people with their own desires. Yuji will actually be able to have a future with Shana that is more than just an endless conflict. To this end, Yuji and the Snake of the Festival are incredibly ruthless. They brutally beat up Shana, seal her power, and traumatize her. They push Margery Daw, one of Yuji's friends and former allies, past the Despair Event Horizon. They prosecute a war that brutally kills off many Flame Haze opposing them. Their underlings are treated as disposable. But they succeed in every last one of their goals, and the world is a much, much better place for it.
In Transformers Cybertron, Scourge and his followers seized power for themselves and after a lengthy war managed to bring peace and order to Jungle Planet, whose civilian populace had long suffered at the hands of feuding groups of raiders. This peace brought through tyranny was not perfect (Scourge's old mentor Backstop observes that Scourge's method treats the symptoms but not the cause), but it was vastly preferable to how things had been.
Aeolia Shenberg in Gundam 00 believes that the human race is inherently corrupt and warlike, and must reform itself to get rid of war... by force, if necessary. It takes him and his shadow organization Celestial Being 200 years to put their plans into motion, but it works. By AD 2500, humanity has evolved into a race of telepaths and are completely free of war... all by Celestial Being's manipulations.
It's rather peculiar, but this viewpoint is virtually identical to the one held by Char Aznable in Char's Counterattack, except Char's methods were far more destructive and he was portrayed as being very much in the wrong in that film.
After being resurrected at the end of Shaman King by Hao and living a few years in the world they were fighting to preserve, most of the heroes agree that he was right and there is nothing they can do about it. The worst part of it is that he sent them back just to show them they were wrong. Played with at the end, because while the heroes admit that the world is much harder to change that they suspected at the beginning, they are still alive and determined to find solutions and fixed it for the better.
Digimon Tamers in the argument of the god like digimon over how to save their world, it turns out the plan of the well intended extremest who acted very brutal towards the child protagonists was the only one they could use in the end. Pity half their world was destroyed. Still, his was the only plan that worked if even temporarily.
Played with in Attack on Titan. The various arguments given against Eren's trial are seen as paranoid ravings, seeing how Eren helped humanity achieved their first victory against the Titans. But Erwin does agree with them that there could be other Titan shifters, and there are.
V for Vendetta averts the trope, implying that the anarchist state V created via his terrorism may turn out to be just as bad a place as the fascist state he overthrew. The film adaptation plays it straight with no fear of a possibly dark future portrayed.
In Watchmen, also by Alan Moore, Ozymandias' plan to trick the superpowers into peace works initially, but it's Left Hanging whether it's going to last for long. In this case, the movie doesn't differ much.
Shortly before the finale (in the comic), it's revealed that the superpowers have both decided that the current tensions are not worth mutual annihilation, and have sat down to negotiate. Ozymandias, busy with carrying out his plan and dealing with the heroes, is unaware of this. He was wrong, because he underestimated humanity's sanity.
Doctor Doom. Several times it has been shown that the world might actually be a better place if he ran things, with war, famine, poverty and disease all things of the past in various alternate worlds and timeliness where he has successfully taken over. Latveria, his country, is also a well-functioning society and, despite its tiny size, a major global power under his rule. This is true also for other comic villains like Magneto or Lex Luthor, but Doom is special because, more than the others, this is one of his core motivations. All three usually end up running an oppressive Police State, to varying degrees but damn it; it's an oppressive Police State that works.
One of Doom's biggest problems has always been that, well, he's always been hung up on his grudge against Reed Richards. Were Reed Richards removed from the equation, Doom would probably have utilized that mind of his in far more constructive means from the very beginning.
Canonical according to "What if the Avengers fought Galactus?" (What If v2 #41). Reed, Sue, Ben, and Johnny all DIE in their test flight. With Reed proven to be something of an idiot, Doctor Doom goes on to become an anti-communist ally of SHIELD.
There are actually multiple alternate universes in which Reed dies and Doom becomes a hero afterward.
As above, Lex Luthor has it in him to be one of the greatest men in all human history and the capacity to solve nearly all the world's problems, most notably in Superman: Red Son where he eventually intitiates a Golden Age lasting millions of years. The hitch? He is so murderously jealous and obsessed with Superman that he won't do any of that until after he kills "the alien", and has frequently endangered the planet trying to do so. And unlike Doom, he doesn't even pretend to himself that if he did this, it would be for humanity's benefit; no, he just likes to show everyone just how much smarter than them he is. As All-Star Superman puts it, if Lex had truly cared about the world, he would have saved it years ago.
After spending a year without powers and out of sight, Superman showed up again and called Luthor on all the great things he didn't do without his nemesis around to "stop" him. "Where's the cancer cure, Lex?"
In the older days of the Superman comics, there was a planet called Lexor that worshiped Luthor as the greatest hero ever, because he had saved their planet. The planet blew up due to Lex shooting at a control tower that kept the planet stabilized. While trying to shoot at Superman. Unwilling to accept his role in destroying his own home and killing his own family, Luthor's hatred of Superman got worse.
Correction, Lex shot Superman only for Superman to reflect it against the newly installed Tower intended to stabilize the planet's core causing the planet's destruction and the genocide of the people of Lexor. It was Superman who failed to accept any of his responsibility for what happened (since but for his traveling to Lexor and ignoring his normal policy to respect to the laws of other planets Lexor would have never been destroyed).
Superman, of all people, demonstrates this in Superman: Red Son when he finally gives into the wishes of others and uses his powers to micromanage the entirety of the Soviet Union (which at its zenith is the entire world except for America and Chile) he manages to stop all crime, waste, corruption, poverty and pretty much every other problem mankind has.
Over the course of the last decade, Cyclops has slowly, but surely, became a Knight Templar to protect the remaining mutants. He's discarded the Thou Shall Not Kill rule, built two military compounds to house the populace (one in international waters), assembled kill squads, and allowed minors to fight on front lines. However, the enemy that pushed him to these extremes, Bastion and the Purifiers, would have killed them all had he not done so, and using these methods he's defeated Bastion, built ties with San Fransisco's mayor to make the mutant populace look a lot better then they used to look, defeated a vampire army and earned the respect of Dracula. Then, when in Avengers vs. X-Men he gets possessed by the Phoenix, he works to make the world a better place, only for him to eventually lose his sanity and kill Xavier during a fight with the Avengers and the X-Men. However, by the end of it, mutants are restored and, largely, everything he was trying to do is done. He does whatever it takes, and he lost some humanity in doing so, but he did it. He only has one regret, that it could have been him to die, not Xavier.
Mentioned in Knightfall. Despite Az-Bats being a complete psychopath and the real Batman having to come back and stop him, the mayor points out that crime's dropped nearly 42% since he came onto the scene. Even more, back during those initial issues, when the real Batman saves the mayor, he realizes that he is needed and tries to get Gordon to stop pussyfooting and really get down to business with the criminals.
The Fanfiction 'Fandom Wars', a multi-universe crossover revolving mostly on characters from or working for the My Little Pony: Friendship is Magic world and its 'Fandom Wars' faction. Originally, they intended to stay out of the war, but communication between the Dimensional Rifts distorted messages and ruined their chain of command, allowing a small group of extremist ponies to manipulate their home world into a corner during the fighting, and forcing them to use a weapon that made their universe swallow the others. The sentient inhabitants of Earth are completely wiped out and reborn sometime later as ponies, and, as Captain Pio had said it would, strife and war were all gone because the ideologies of the world before were almost completely wiped out.
Renegade Reinterpretations recasts Cerberus in this light: With human survival genuinely on the line, no line of research can be ignored, no matter the ethical concerns.
And in ThorTheDarkWorld this gets spun: facing Odin for his actions on Earth in the The Avengers, Loki claims he is merely following in the footsteps of Odin's father Bor and of Odin himself, and that he would have been more suited to the crown than Thor. Notably, Odin doesn't dispute this, and Odin's actions for the rest of the film, including his cold-blooded strategy for dealing with the Dark Elves, makes this clear to Thor. Thor realizes that he'd rather be a good man, protecting the innocent and doing what's right, instead of a king who'd have to be willing to sacrifice others and other pragmatic decisions. So once again Loki gets proven right, this time not because Thor wasn't ready, but because Thor realizes he wants to be a better person than a king can be.
Played with, sort of, in Birth of a Nation: complete racial egalitarianism is deemed ‘extremism’ in the film. In the film, this attitude leads to a violent uprising on the blacks’ part, lead by a mulatto; the creator vehemently denied being racist, so he probably didn’t actually see that view as extremist, so... Well, enjoy the Mind Screw.
Senator Kelly from X-Men might be a complete Jerkass and fear-monger, but at the same time, given what Magneto gets up to during the course of the films and that we later learn his aide was killed and impersonated by Mystique for "quite some time"... he has a point.
In X-Men: Days of Future Past, Bolívar Trask said "You are not fighting a skirmish on the other side of the world, you are fighting people who could be amongst you, in your offices and homes, and who may have already taken over. And then you will have suffered a worse defeat than in Vietnam". Now jump forward to the climax, with Magneto surrounding the White House with a full stadium levitated from across the state and with the life of the President in his hands, and with another mutant already infiltrated among the President's most trusted people... and say again that Trask was exaggerating, or that his concerns were unjustified. Of course, it was his actions that provoked them to do this, so it's a Self-Fulfilling Prophecy.
The Lord Ruler of Mistborn is a dictatorial Evil Overlord ruling as King and God over The Empire, but is also the one force for stability holding humanity together After the End, and the only thing standing between the local Omnicidal Maniac and his goals. The heroes' perspective of him changes throughout the story: During his life, he's viewed as a monster who needs to go down but after his death, this opinion is gradually revised to that of an Anti-Villain without whom the ultimate victory would not have been possible. Vin even offers him quiet thanks once she comes to understand how much he did to keep them all alive.
Discworld's Lord Vetinari is fond of using this defense as it relates to some of his... odder plans. Commander Vimes, however, notably believes that just because Vetinari's way of doing things may work, doesn't make them right per se.
However, Vimes shares a common opinion with the vast majority of people and institutions in Ankh-Morpork: as much as they may disapprove of Vetinari and his methods, they realize it's better than the alternative. Vimes, at least, wouldn't hesitate to arrest Vetinari if he believed Vetinari had committed an actual crime (proven by the fact that he didn't hesitate when it seemed exactly that had occurred).
The White Council (specifically, the Wardens) in The Dresden Files universe qualify as this in one of their roles. As enforcers of the Laws of Magic, they hunt down and execute any violators after, usually with only a cursory trial. They openly admit that they use execution in preference to other options, such as training or rehabilitation. Harry frequently rants about how unfair and unjust this practice is, but is ultimately forced to admit that their tactics have prevented the rise of innumerable dangerous warlocks over the centuries.
A big part of the reason Harry sucks it up is that he knows that black magic, even when used unintentionally, is addictive, and leads to more and more.
The political nature of the White Council also applies. By removing themselves from non-magical affairs, the Council has minimized the formation of internal factions and the chance of splintering due to internal conflict over events in the non-magical world.
One word: Martin. And when we say 'extremist', we are not kidding.
Ender’s Game: Peter Wiggin is cast as a nascent sociopath and abusive brother in the beginning of the series. By the time the third book rolls around he is "Peter the Hegemon," the man who united humanity via Machiavellian politics, the vilification of his own brother Ender ("the Xenocide") and... Sock Puppet bloggers. Yay for sociopathy!
The later books do a good job of explaining that. His character in Ender's Game is just what Ender could see - and Peter got some character development. Although The Extremist Was Right is still applicable.
Graff and Rackham also have shades of this trope.
A bit unusually for this trope, Graff (and probably Rackham as well) is fully aware of how insane and extreme his methods look to outsiders (i.e. everyone but him). Graff doesn't bother sugar coating anything, he doesn't even guarantee his plan will work. He just thinks it's the fastest way to assure there's a leader ready for the next war against the Buggers.
Extremism seems to be the defining trait of successful Hands of the King: Tywin Lannister was absolutely ruthless to anyone who dared oppose him, and he successfully kept the peace under King Aerys II for twenty years. In the Tales Of Dunk And Egg, Lord Bloodraven was equally ruthless - and managed to stop the Second Blackfyre Rebellion without bloodshed. One the flip-side, more reasonable Ned Stark and Jon Arryn were both murdered, though for reasons and by people mostly unrelated to the way they ruled. We don't know exactly how efficient Jon Arryn was.
Though he was definitely one of the best Hands of the King of the kingdom, Tywin's ruthless approach to the Civil War, including unleashing Gregor Clegane or orchestrating the Red Wedding ultimately destabilized the country further, and resulted in many civilian deaths. Especially the Red Wedding, which temporarily halted the war, but ultimately fueled the North's motivation to resume it. Also, his abusive behavior towards his family was partially responsible for the damage caused by Cersei and Joffrey's respective rules, and ultimately lead to his own death.
The rationale of the Thallonians in Star Trek: New Frontier. The Thallonian Empire brought peace to the warring races of their sector by conquering them all, forcing squabbling factions to settle on different planets, and generally ruling with an iron fist. They were a harsh and often brutal regime...but they did keep the peace. With the empire gone, Si Cwan rightly fears all the old conflicts will start up again, throwing the region into chaos.
David Gerrold's Yesterday's Children keeps it ambiguous whether the first officer is insanely chasing a hallucination or conducting a Batman Gambit against an unseen foe. Then it works out just fine in the span of about a page.
The Redeker Plan in World War Z was a strategy that required the world's governments to use a good chunk of their civilian population as bait to distract the zombie hordes, while the nation's military, industrial and political figures, as well as the rest of the population, regroup in a single safe zone... and it works. Oh, and the plan was originally created by apartheidSouth Africa to deal with a black revolution.
Emperor Ezar in the Vorkosigan Saga , who first started an unprovoked war and then lost it deliberately, in the process almost driving his most loyal and incorruptible supporter to suicide, killing thousands and bringing about the rape of several women as a by-product. The reason? The Emperor believed(not inplausibly) that his son was so completely insane and corrupt that the only other choice would be to ruin the realm with a bloody civil war just to get rid of him. As the final result was that Barrayar in fact was able to evolve into a period of peace, prosperity, and stability, one might well say he was right. Sort of.
In Reamde, the isolated community of survivalists turns out to be perfectly suited to fight the terrorist assault that really does happen.
Rob Pierre in the Honor Harrington novels figured that the only way to reform the People's Republic of Haven was to first murder the corrupt Legislaturalist government, then lead them in a war against a foreign enemy, thus giving the Dolists (who had spent their lives on welfare) a reason to actually work. He caused the death of millions, and he himself was ultimately killed by a civilian uprising, but his work did help strengthen Haven, paving the way for Eloise Pritchart and Thomas Theisman to overthrow his successor and restore the old Republic. In the end, Pierre would probably be happy with how it all turned out.
Word of God has confirmed the core of the Legislaturalists were Alpha Lines and a major part of the Mesan plans were to use the Haven fleet to topple the Solarian League, making Rob S. Pierre practically a saint.
In Worm, several of the super-villains are these - but in the end, the biggest, baddest one is Skitter.
Live Action TV
Police Major Bunny Colvin from The Wire decides that the best way to curb violence in the streets is to set up Hamsterdam, a zone for drug dealers to ply their trade where the police would not bother them. Essentially legalizing drugs in his district as long as the dealers don't stray from the free zone. While this is a questionable action, it really does lower the rate of crime and felonies by as much as 14%, and the quality of life gets better as a result. And it's shut down by PR controversy and Colvin is unceremoniously fired from the police force.
The Hawaii Five-O episode "The Box" starts off as a criminal's attempt to escape from prison by taking a bunch of hostages and demanding to be let go. However, after McGarrett exchanges himself for one of the hostages, buys more time, and generally keeps him talking, it turns out that he was pushed to this by the genuinely squalid conditions in the prison, and (with a few close calls — he is a criminal waving a gun) he eventually settles for getting the word out, which is apparently a total success.
In Star Trek: Deep Space Nine, a secret organization in Starfleet poisons the entirety of the Great Link, a species of shapeshifters who the races of the Dominions see as gods (Or at least rulers). Their reason for this is that The Dominion is the greatest threat The Federation has ever faced, and so genocide would be an acceptable solution to the problem. In a show where every cast member has engaged in highly morally questionable acts in order to do good, every one of them sees this as going too far. And yet, it is only the promise of the cure for the disease that convinces the Founder in charge of the armed forces to surrender peacefully when she is captured. Under any other circumstances, she would have ordered her soldiers to fight to the bitter end, which would have resulted in countless more casualties, in what was already the largest battle in the history of The Federation.
Section 31 didn't want the cure to be found. They tried to stop Bashir from finding it and tried to interfere when they thought he had. The Federation Council considered giving the cure to the Founders but voted not to. They could have offered to trade the cure for the Founders' surrender, but the Founders still believed they could win the war at that point, so it is highly unlikely they'd have accepted (though one can ask whether it would have hurt to try). It also should be noted that Section 31 used Odo as a carrier to spread the disease to the others. Odo had been a long time Federation ally who sided with them against his own people, and they not only infected him but tried to prevent Bashir from getting the cure. However, it was pretty clear that Section 31 did not intend for Odo himself to get sick. Sloan (of Section 31) might even have given Bashir the cure if he had been 100% certain that it would not be shared with the Founders the Federation was fighting. While Bashir obeyed Sisko's orders not to disclose the cure to the other Founders after he got it, one can understand how they wouldn't trust Bashir even had he made a promise to cure Odo and only Odo.
In the episode In the Pale Moonlight, Sisko decides to enlist Garak to help in getting the Romulans to join the Federation in fighting the Dominion. Garak's plan is... morally questionable, to say the least, and causes Sisko to question what's more important to him: his values or gaining valuable allies? In the end, Garak's plan works, and Sisko, despite reservations, decides to keep the truth a secret.
In Season 6 of Supernatural, Castiel teams up with the King of Hell to bust open Purgatory and absorb the souls trapped there (torturing and killing many innocents and betraying his friends on the way) so he will be powerful enough to defeat Raphael, who is trying to restart the Apocalypse. In the end he succeeds and kills Raphael... then promptly declares himself God.
In the Star Trek: The Next Generation episode "The Wounded", Captain Picard is assigned to stop Captain Benjamin Maxwell, who has been conducting unauthorized attacks against the Cardassians because he suspects that they are re-arming despite their peace treaty with the Federation. Picard succeeds in stopping Maxwell, but ultimately notes to Cardassian Gul Macet that despite his own claims, Maxwell was indeed right about a re-arming Cardassian fleet.
In "The Day of the Doctor", the Tenth Doctor the Eleventh Doctor are allowed through the time-lock to confront the War Doctor as he prepares to raze Gallifrey. Yet despite their centuries of regret, it turns out that they still agree that it was the only thing to do and they came back so that the War Doctor wouldn't have to do it alone. Subverted at the last minute, when the Eleventh Doctor realises that they have another option they didn't have the first time, to use Tricked Out Time to rally all thirteen of his incarnations to fake the destruction of Gallifrey, letting the Dalek's wipe themselves out from their own crossfire when the planet disappears.
Traveller: Cleon Zhunastu was a Magnificent Bastard who built the Third Imperium by a series of schemes worthy of the greatest of villains. And the Third Imperium became a Benevolent (sort of) Federation that brought about order and stability.
In Mage: The Ascension, the Technocracy is generally considered the villain of the setting for imposing their outlook of science on the world, crushing belief in magic, and doing so utterly brutally. Said science allowed the Muggles a "magic" of their own to use, while actual magic includes extra-dimensional and alien horrors. In a setting where belief shapes reality, there is good reason to believe that "reality deviants" could undo the laws of physics. I hope you weren't using those molecular bonds in your torso or planet.
Only molecular bonds are not what is holding matter together in a reality shaped by magical beliefs. When you grok that, you'll see that "science" does not mean in the oWoD what it does in our universe and the Technocracy are not right. This is not to mention that Technocracy are less about Science and more about Control. There is a reason that the Etherites and the Virtual Adepts are part of the Traditions.
This is a running theme in the world of darkness: the faction you belong to as a player are not the "good guys", they're monsters that can occasionally rationalize being monsters by pointing at the sporadic occurrence of worst monsters. In vampire and werewolf, you eat people and the good guys are the hunters that kill you and the oppressive ancient overlords and "evil" spirits that keep your numbers in check. In changeling the good guys are the normal humans that you intentionally torture into madness or to death for your own amusement. Basically mage is the same deal, it's just slightly more obvious because the good guy faction, the technocracy that has found and enforces an actual balance between the advancement of mages and the safety of baseline humanity, also happens to be the only faction that can actually stand up to a cabal of mages and a lot more is resolved through investigation in Mage than in other systems. So you tend to run into them more than anything else and get into their backstory and motivations more than, say, the inquisition in Vampire.
In Vampire: The Masquerade, at the founding of the Camarilla there was concern that the insane Malkavian vampires would become a threat to the Masquerade by virtue of their power to induce madness, "Dementation". Six of the most ancient Malkavian vampires sent out a telepathic summons, forcing almost all Malkavians to travel to one town in Eastern Europe. After they had gathered, the same six subjected almost every Malkavian in the world to a systematic Mind Rape to make them less likely to become threats to the Camarilla and more likely to be accepted as members of the group, even replacing Dementation with direct Mind Control powers. Potentially, this is how Clan Malkavian became as respected as it is.
For all the gripes against the actions of the Bronze Faction (many of which, admittedly, push the boundaries of highly illegal into verging on atrocious), they saved Creation.
If you believe in the Vision of Gold, you do not agree.
The same goes for the Scarlet Empress. Sure, she did some pretty bad things to gain control of the Sword of Creation, used it to make herself the undisputed ruler of what she made the most powerful empire in the world, and created a series of oppressive vassel states and a ruling class fixated on self-aggrandizement and low-level infighting, but she also used the Sword to save Creation from the raksha, made sure they could never come back to finish the job, and spared Creation the constant intense (civil) wars that characterised the regime preceding her reign.
The entire POINT behind the Deadly Decadent Court was to distract a few thousand Super Soldiers from trying to make trouble in the empire by giving the Terrestrial Exalted Luxury, worshipful admiration from the populace... And to keep them busy. The Empress even designed the infrastructure of the Realm to make it utterly impossible for it to function without her (There had been a few attempts at overthrowing her... which ended in having the Sword of Creation turned on the rebels). Leaving the Nobles to squabble over bits and pieces of influence and power within the Realm which was more or less manageable. This worked for over seven centuries... until she vanished and the entire system starting plunging rapidly towards Civil War.
Official Solar Exalted characters such as Havesh the Vanisher, Mirror Flag and especially Lyta show quite blatantly why the Immaculate Faith isn't entirely wrong to refer to Solars as evil.
The Brotherhood from Mutant Chronicles takes pretty much everything about the Catholic Church throughout history, good and bad, and cranks it Up to Eleven. But then again, when you live in a world where battles with the Legions of Hell aren't even headline material anymore, the "bad" comes across more like "harsh but necessary".
In Eberron, the gnomish country of Zilargo dispenses with any kind of due process in favor of letting its extensive network of secret police, the Trust, constantly spy on citizens and foreigners alike and intimidate anyone even considering a crime out of the idea with whispers from the shadows. And if that doesn't work? The would-be criminal generally "disappears" before they can actually commit a crime. The result? A happy, fearless populace and the lowest crime rate in all of Khorvaire.
Also a case of Blue and Orange Morality. Spying on everyone else is considered the national past time and everyone assumes that they are being watched at all times. So that means any overt criminals are also Too Dumb to Live.
Urinetown features an oppressive corporate dictatorship that charges the citizens of the titular town for the privilege of using the bathroom. The citizens eventually rise up and overthrow the company, only to find that the bathroom rationing was preventing overuse of the town's water supply. As a result of the revolution doing away with the restrictions, everyone dies of dehydration.
The titular Halo rings were built by the Forerunners to scour the entire galaxy of life in hopes of starving a virulent parasite. Yet their head of the military, the Didact, refused to activate them and tried to turn to other solutions such as super-intelligent AIs, which turned against him, or experimental cures, which mutated him. His final plan was to convert all humans in the galaxy into robotic soldiers that serve him. His own wife has to imprison him to stop this from happening. Of course, as we see, the Halo solution does eventually let the parasite escape and attack the galaxy again.
The Spartan supersoldiers were kidnapped children who were indoctrinated for years and trained under The Spartan Way to become humanity's most elite warriors. Why? Because The War of Earthly Aggression was increasing to the point that it predicted to end with a new Dark Age. Then came the Covenant, and Spartans were the only consistent game-changers. Finally the war was won and only because of Spartans, with the rest of humanity to pick up the pieces and debate with the arrested scientists over whether their experiments were justified.
Jowy Atreides in Suikoden II joined the other side in a complicated plan to kill Luca Blight. This resulted in quite a few massacres and an entire city getting their souls sacrificed. However, Luca Blight is literally a One-Man Army and it's... questionable if his Rasputinian Death would have been possible if he had not done so.
Similarly, Suikoden V has Sialeeds betray the rebels just when it seems they're about to win a decisive, possibly war-ending victory. Eventually, it's revealed that she did this so that all of the corrupt nobles, including those who don't back the currently-ruling Godwin faction, can be eliminated. And since a traitor was responsible for it happening, there's no way the brutality can breed resentment against the rightful queen after her restoration to power.
Command & Conquer: Kane. Despite his genuinely horrifying crimes in the previous games, by the time Tiberian Twilight takes place, his plan is the only one that has any chance of saving the planet. Even the GDI Council bitterly recognizes this.
Bhelen of Dragon Age: Origins is a backstabbing, dishonourable noble who uses all kinds of underhanded tricks to try securing the throne of Orzammar, even going so far as to backstab the player in the Dwarven Noble origin. However, if given the crown he uses his position to grant basic rights to the casteless and destroys the venomous system of Dwarven politics by dissolving the Council, becoming a benevolent dictator.
Bhelen also happens to be following in his paragonic ancestor's footsteps. Aeducan did something quite similar; while the nobles were all bickering over whose thaig to save from the Darkspawn menace, Aeducan seized control, and sealed off Orzamaar, which effectively saved it at the cost of abandoning the thaigs.
Avernus sacrificed his fellow Grey Wardens in horrific experiments in order to better understand the properties of the Taint, spending two centuries obsessively working on a way to improve upon and better refine the Joining Ritual. The result of this is a concoction that allows Wardens to directly tap into some of the power within their own Tainted blood.
Much like Avernus, the Architect in Awakening killed an untold number of people in brutal experiments, attempting to use Grey Warden blood to create intelligent, self-aware Darkspawn, cut off from the call of the Old Gods. He reveals that his motivation is not to rule them or raise an army, but simply to free his people from being mindless slaves to the Archdemons and help them find a place in the world. The Warden can sympathise with his goals and even broker an alliance with him.
In Dragon Age II, supporting material seems to lean into the direction that escalating the conflict between the Mages and the Templars into a full rebellion was ultimately the right thing to do, as the status quo only kept weakening the mages position. Even though Anders' bombing of the local Chantry with half a dozen priests still inside it was way out of proportion, which also lead to the senseless death of the mediating local high priestess.
Sydney Losstarot of Vagrant Story. He wants to save the world by creating an heir to the power of The Dark, thus keeping it out of the hands of the people who would abuse it.
An example shows up in Tales of Phantasia, but it's not that game's villain who gets vindicated. It's the villain of the game's prequel, Tales of Symphonia. SymphoniaBig Bad Yggdrasil created the dual-world system, deprived both sides of mana, and stuck the worlds in a state of Medieval Stasis in order to prevent Magitek proliferation, which he believed would lead to another great war of the same type that destroyed civilization when he was a child. In Phantasia you come cross the ruins of magitek civilizations dating after the events of Symphonia. Logs show that, you guessed it, without Yggdrasil's system, civilization destroyed itself in a Magitek war and underwent a Cataclysm Backstory, sticking the world right back in Medieval Stasis.
In Wild ARMs 2, it turns out that the game's entire plot was part of a Genghis Gambit by Irving, all so that he'd have the opportunity to sacrifice himself and his sister to create a physical body for an encroaching parallel universe, which the heroes would then kill. He succeeds in saving the entire universe (and probably countless others), but leaves the heroes wondering whether what just happened counts as a "win".
Fallout: New Vegas: The very brutal empire known as Caesar's Legion successfully unified eighty-six warring tribes and turned it into a safe regime for its subjects. Safe does not mean free, except if you have a dick and don't have a slave collar.
The NCR has heavy taxes, often would rather shoot first and ask questions later, and limits water to the point where most barely have any to drink. However, it's one of the best places to live.
Mr. House is a Machiavellian schemer who can't stand sharing power with anyone and ignores those who aren't useful to him, but if he wins, he turns New Vegas into a safe, stable and prosperous state in its own right, with comparative social freedoms. He furthermore goes on to revive advanced pre-War level industry so that humanity may expand into space and no longer be dependent upon what is left of Earth.
The Boomers are an intensely isolationist and xenophobic society of ultra violent gun nuts. However, they also live in the Mojave Wasteland. Their paranoia has led to Boomer territory being arguably the safest and most self-sufficient around, with morale and quality of life abnormally high by Wasteland standards.
In his route of Yggdra Unison, Gulcasa conquers the world, becomes the first Emperor (read: dictator) of the Grand Bronquian Empire, and proceeds to rip down class barriers and save the weak and the poor. Thousands of years later, Bronquia is still going strong, and Gulcasa is a beloved historical figure. (It helps that Gulcasa is Gulcasa.)
The end result of the first Prototype story was chiefly due to internal forces conspiring within Blackwatch to subtly manipulate Alex into doing what they could not overcome on their own, and hence fulfilling their mandate.
The final DLC of Mass Effect 2 has Shepard being forced to detonate a Mass Relay and sacrifice a solar system of three-hundred-thousand people in order to slow down the arrival of the Reapers. While this works, the rest of the Galaxy considers the Reapers to be a myth, with the upper echelons of power discredit Shepard as delusional or worse leading straight to...
...Mass Effect 3, which picks up several months later. Shepard is now disharged from the Alliance and going to trial for his/her actions, which gets interrupted when the Reapers finally descend upon Earth. Unfortunately, by the time we get to see the Council, the invasion is well underway, so we miss their initial shocked/horrified reactions to the fact that Shepard was right all along. Amusingly, it's the resident air-quoting Turian Councillor Sparatus who ends up being the first of the Councilors to offer Shepard aid in the form of vital intel.
Interestingly though, the same upper echelons of power who are busy trying to discredit Shepard never actually revoked Shepards SPECTRE status in the interim between Mass Effect 2 and Mass Effect 3...
It's somewhat telling that even after being proven right, Shepard still remains a Hero with Bad Publicity due to their actions;
The enemy are referred to as "Reapers", a term once used by the disgraced Commander Shepard.
As a corollary to that, The Illusive Man. Indoctrinated though he may have been, his belief in controlling the reapers is one of the three ways Shepard can choose to save the galaxy (even though The Illusive Man himself could never have taken control). Additionally, the 'Control Reapers' Ending is the only one wherein the Citadel isn't severely damaged, possibly saving many lives.
In Mass Effect 2, Maelon, a former student of Mordin's, is revealed to be conducting brutal experiments on live test subjects in an attempt to develop a cure to the Genophage. After dealing with him, Shepard is given the choice of whether to either preserve the data or to destroy it. However, the data becomes vitally important in the third game to ensuring the survival of the last female Krogan immune to the genophage.
In the Citadel DLC of Mass Effect 3, one of the videos you can see from the Citadel's historical archives show that the first Spectre was a Salarian operative who used 30 civilians to flush out a criminal, whose ruthlessness in getting the job done managed to impress the Council of that time.
Isran from The Elder Scrolls V: Skyrim DLC Dawnguard. Former Vigilant of Stendarr, founder of an order of vampire hunters, is a racistdick, repeatedly kicks the dog in his dealings with friendly vampire Serana, and admits that hatred of vampires keeps him strong. Knight Templar? Go over to see the vampires of Clan Volkihar and say that his view is unjustified. The vampires of Clan Volkihar are savage, backstabbing, cruel monsters who view humans as a food source, and have no qualms about killing us or even their fellow vampires if they get in their way. As bad as he is, he is not dealing with Friendly Neighbourhood Vampires and is protecting people from a dangerous threat. If the player goes through with the Dawnguard story path, he becomes much less extremist in his views, going so far as to keep Serana in the Dawnguard and thanks her for her aid in bringing down Clan Volkihar... however begrudgingly he does it.
Isran was thrown out of the Vigilants of Stendarr, believing that they were becoming too soft, while they considered his methods too extreme, even for them! However at the start of Dawnguard, Isran is alive and operating out of a heavily fortified castle, while most of the Vigilants were wiped out when the wooden lodge serving as their headquarters was burnt to the ground, by the very vampires Isran warned them about!
In Der Langrisser, Elwin fulfills this trope in the Independent storyline. He turns against the Light in an attempt to bring peace for everyone in El Sallia, both humans and the Demon Tribe, and does so by destroying both warring powers (Kalxath, stronghold of the Light, and the Rayguard Empire) and the wicked Bozer, capping it all off by killing the goddess Lushiris. After all of this, he becomes known as "the King of Peace."
In BioShock Infinite, Daisy Fitzroy holds a young kid (later confirmed as Jeremiah Fink's son) hostage at gunpoint, believing that the Founders are like weeds and that the only way to get rid of them is to "pull them up from the roots", to kill the children before they follow in their parents' footsteps. Strangely, this is the same logic that Booker DeWitt and Elizabeth use to get rid of Zachary Comstock near the end of the game, when Booker has various alternate reality versions of Elizabeth drown him before he could make any decision that would result in the creation of Comstock.
In Injustice: Gods Among Us, while a big deal is made of Superman making himself the dictator of the world, he's evidently managed to severely weaken Ares, God of War from the peace he's created.
Drakengard 3 features yet another villain protagonist, Zero, who has no trouble slaughtering hundreds of mooks and families and no sympathy for the consequences of killing the ruling factions, even before she obtained the power of Intoners. And then you find out her past: her pre-Intoner life was one long Corrupt the Cutie in a Crapsack World (mother abused and sold her, best friend betrayed her, boyfriend ran and backstabbed her when she got an incurable disease), and those Intoner sisters of hers that she plans on killing are actually artificial humans, created when she tried to commit suicide, and that any Intoner will eventually lose control of their powers and sing the song to end the world. She plans on committing suicide the right way after dealing with them. To top it off, Intoner is the definition of GROTESQUERIE QUEEN. As in, the Big Bad of Drakengard and the apocalyptic disease-bringer of Nier.
Tarvek shows the same tendency, though so far hasn't had an opportunity to apply it on a large scale: "I'm not proud of that, but time was running out. And I did it!". Though he succeeded at first, Laser-Guided Karma eventually hit him hard, and plans similar to his own plans to rule Europa are falling apart around his ears.
In later editions of the comic Klaus is incapacitated and/or dead, the Long War has resumed, perhaps even more violently, as rulers squabble over pieces of Klaus' empire. How this will shake out remains to be seen, but the Aesop seems to be that all dictatorships, even benevolent ones, only last as long as they have a strong leader to keep everyone in line.
Petey from Schlock Mercenary: He is trying to keep organic lifeforms in the galaxy from exterminating themselves by dealing with the big threats to their existence for them (because they lack the will and power to do so), not caring a whit how many organic toes he has to step on in the process of doing it.
For that matter, the Gatekeepers suppressing teraport technology for millions of years and killing off several thousand times the Milky Way's population in gate clones worked in appeasing said Omnicidal Maniacs and keeping them from destroying the whole thing. It is a very fortunate thing for all involved that by the time our heroes (inadvertently) re-invent the teraport and challenge the Gatekeepers, they also prove potent enough to stave off the threats the Gatekeepers were protecting them from.
Lord Doom, one of the biggest of the big bads of the Global Guardians PBEM Universe used mercenary soldiers and supervillains to drive out the British government from Bermuda and take over the island as his own kingdom. He rules it with an iron fist and its people have very little in the way of civil rights as most Americans know them. That said, twenty years after the conquest, the island has a 0% poverty rate, infant mortality rate, and illiteracy rate. The average life span of one of Doom's subjects is close to a hundred years due to medical advances made by the Supervillain, and nearly all adults have a college education. The takeover was intended to give Doom a "social laboratory" in preparation to his eventual conquest of the world, and it worked!
In Atop the Fourth Wall videos, Lord Vyse has been going from universe to universe to stop "the entity" by imposing dictatorial rule when many of them didn't believe him about the danger. He's been rather successful in his attempts, finally trapping it in Linkara's universe.
Cartman in the South Park episode "Die Hippie, Die".
While Teenage Mutant Ninja Turtles' Agent Bishop has done a lot to earn the turtles' ire, and is generally an unscrupulous bastard, there's little doubt that he's generally very good at his job of protecting Earth from alien invasion, and has managed to do it for more than two hundred years.
In the 10 year anniversary episode of Powerpuff Girls, Mojo-Jojo finally takes over the world, and he ends world hunger, wars, and disease... with absolutely no consequences. The Powerpuff Girls apologize for stopping him all those years, but he eventually gets bored and decides to cause mayhem so he can fight them again.
Justice League probably gets as close to this as possible for a kid cartoon with the Justice Lords, a Knight TemplarAlternate Universe equivalent to the titular League, who revoked their Thou Shalt Not Kill dogma, removed free speech, united all world governments under their rule and lobotomised all their supervillains (and, reading between the lines, possibly a few rebellious superheroes as well). End result:
Their world is bright and clean and has no crime or war, and the Justice Lords keep constant surveillance over the world to the degree that even natural disasters cause minimal casualties, which even has a result of boring the Lords out of their mind for lacking problems to solve (which is pretty much what leads to the creation of the door). Compared to the League's world, with the constant murder and terrorism, superhuman experiments, corruption, and threats such as an evil godlike alien who rules an entire planet, a godlike robot who has the power to destroy an entire planet, hundreds of dangerous villains ranging from evil geniuses to superpowered thugs (all of this continuing for decades up to Batman Beyond), the League's Earth going through three different alien invasions and an unspecified "Near-Apocalypse", the Lords's world would seem safer to many, if not ideal.
On the other hand, people can be arrested for such things as complaining too loudly about their meal at a restaurant, free elections are suspended as a "temporary measure", and student protestors flee from the sight of Hawkgirl and Green Lantern. Lois Lane describes free speech as "all but dead" as a result of the Lords' actions.
The end result is the victory of the 'traditional' heroes when the Justice Lords attempt to clean up the League's Earth (out of what appears to be nothing more than the goodness of their hearts) and the message that 'sometimes Utopia Doesn't Justify The Means', but the writers professed the occasional trouble at giving the League the obvious moral high ground.
Parodied in a fantasy episode of The Simpsons. Bart as David loses to Goliath's son, Goliath II (Nelson) and spends years training for a rematch while Goliath II sets himself up as king. When David finally returns and defeats Goliath II, the locals angrily tell him that Goliath II was the greatest king they had ever had, building hospitals and schools and ending hunger and unemployment. They form a mob to take revenge on David, but the police (also established by Goliath II) take him away for murder/regicide and control the crowd before anything can actually happen.
Transformers Animated: The Autobots do a lot of questionable things to win the war, and though not much of it is onscreen, its established that war itself is an ugly thing. Ultra Magnus commissions large fighting machines with severely limited intelligence so they can kill enemy soldiers and not question the morality of it, also so they'd be easier to control. Prowl was shown to be arrested for not participating in the war and forced into the Autobots side. The Autobots action are against the Decepticons, who've destroyed a few planets, left one planet a flaming husk, and commissioned far more WMD's. They've shown a willingness to unleash terrible chemicals in biological warfare, regardless of the effects on the environment and their own soldiers. The Autobot's actions lead to present day Cybertron which is peaceful, prosperous, and has technology connecting them to dozens of other planets all over the galaxy.
The show also makes it clear when extremism is needed and when it's excessive. Ultra Magnus's actions ended the war, in-spite of people like Ratchet thinking he's taking things too far, and he was able to transition to a peace-time ruler. When Sentinel Prime takes over, he makes Cybertron a police state, and strikes against the Decepticons without considering all options. His inability to listen to reason nearly blew a hole in the planet.