Many of the villains in the various Dragonlance novels are this. Two of the most famous are the Kingpriest (whose goal was to eradicate all evil from the world and resulted in the Cataclysm) and Mina (whose desire to restore gods to the world after they vanished again caused the War of Souls debacle).
Rob S. Pierre and (to a much-lesser extent) Oscar Saint-Just, both of whom embraced tyranny in order to keep Haven from collapsing under the strain of a losing war that their predecessors had started, but that they could not themselves end. One of the filksongs from the CDs puts it perfectly:
"Rob, you are riding a tiger; how are you going to stop?"
The irony is, he'd probably be quite happy to see what Haven has become.
Word of God is Mesa is this. They have a very good point that Transhumanism is the best solution to many issues, and that Beowulf is horribly conservative due to cleaning up the Final War's biowar. The problem is they went into hiding for so long that they lost touch with reality and think they have to convince the galaxy with force that they are right.
Bernadus van Dort was this, with emphasis on the well-intentioned part. His goal was to save his world from being gobbled up by the Solarian League, by founding the Rembrandt Trade Union and building up its economic strength. His methods involved getting the best trade concessions from the various worlds of the Talbott Cluster by whatever means necessary, including extortion. Had it not been for the Lynx Terminus, the ultimate end goal would have probably been uniting the Cluster into a single star nation under the RTU banner. When the Lynx Terminus was discovered, he immediately abandoned this plan in favor of getting the whole cluster annexed by the Star Kingdom of Manticore, which worked out much better for the Talbott Cluster anyway.
In Micah E. F. Martin's "The Canticle", Jonathan Servitor is an inquisitor tasked with rooting out heretics and the undead in the last city on Earth. Given, there are high stakes, but Jonathan is nothing short of brutal in his pursuit of justice.
InspectorJavert just wants to uphold the law and catch criminals. Fair enough. His obsessive nature and strict "by-the-book" attitude are what ruins it.
Tam Lin in House of the Scorpion attempted to assassinate the prime minister of an unknown country, presumably the United Kingdoms, judging by his accent and appearance, but ends up taking out 20 young children on a school bus who were too close to the blast. He never forgives himself and later commits suicide by drinking wine that only he knew was poisoned.
Literary example of a Tragic Hero who takes his mission much too far: Alexandre Dumas' character Edmond Dantes, in The Count of Monte Cristo. The self-styled Count, having escaped prison after many years of undeserved confinement, devotes himself obsessively to taking revenge on those enemies who framed him and ruined his life. For most of the book, Edmond is able to ignore the fact that the grand machinations of his vengeance are heaping danger and grief on numerous Innocent Bystanders as well as the guilty.
Captain Vimes from Discworld spends much of his time trying not to become this.
His ancestor, Old Stoneface was this trope. He lived in a time when a Well-Intentioned Extremist was sorely needed. In case anybody wonders, he was modelled after Oliver Cromwell. Plus, his birth name was 'Suffer-not-Injustice' Vimes. It seems that he lived up to it.
In Terry Pratchett's Only You Can Save Mankind, the Gunnery Officer of the Scree-Wee cares about honor more than life and attempts to force the final battle into being fought despite the fact that it could easily be avoided. On the other side, Johnny has to spend a long time persuading Kirsty to try to talk to the aliens instead of simply shooting them all.
The antagonist corporation serving as a front for eco-terrorists in Rainbow Six by Tom Clancy, who plans to kill almost everyone on Earth to allow nature to take over. In the end, Clark has them stripped of all gear and left to die in the jungle. Protests ensue from the villains. His response? "You wanted harmonize with nature. Go harmonize."
The Cavazan Empire, aka the "Saints", in the Prince Roger series by John Ringo and David Weber fit this trope. Hardcore deep-ecologists who keep the majority of their populations penned up in cities operating at low tech levels to avoid "despoiling Nature", who carefully ration everything, including medical care, to "control pollution" (read: control population), and who want to force the rest of the Galaxy to live the same way. To facilitate this, they are willing to conduct generations-long terrorism/subversion campaigns against all their neighbors. Their (hereditary) leaders live much safer and more comfortable lives than the common "Citizens" of their polity.
In the Spaceforce books, Ashlenn’s father Corusval is passing secret research to, as he thinks, the United Worlds of Earth because he fears the sinister Republic of Daros is arming for war against the Empire and the Union. He wants the Earthers to share the Taysans’ technological advantages. Jay admits that he's probably right, then summarily executes him anyway.
General Sarov from Skeleton Key wants to use a nuke to make it look like a a submarine yard accidentally exploded, so Russia could get a stronger Government.
Damian Cray from Eagle Strike. His plan is to hit various places with missiles, killing thousands of innocent people...in order to destroy the drugs fields. His rationale being that he will kill thousands to save millions.
Force Three from Ark Angel is a terrorist groups dedicated to helping the environment though this turns out to be just be a cover.
Help Earth in the CHERUB books is a similar eco terroist group.
Kurda Smahlt of The Saga of Darren Shan does this when he plans to use the night of his investiture as the night of the Vampaneze invasion and take-over of Vampire Mountain, all in order to bring the two warring clans together, even killing one of his best friends in the process. He is found out and stopped, though. If Darren hadn't found out about the plan, however, chances are that the whole War of the Scars would've been averted.
The young Albus Dumbledore and his good friend Gellert Grindelwald, whose slogan was, "For the greater good." After a tragic accident, Dumbledore revised his attitude. Grindelwald never did.
This can also be said of Salazar Slytherin's fear of Muggle-borns due to how, during his time, Wizards were facing a great deal of persecution. He feared that Muggle-borns or their relatives might turn on them, so it was better to not teach them.
Chamber of Secrets had Dobby performing magic in Harry's house, blocking the entrance to Plaform 9 3/4, and enchanting a Bludger to go specifically after Harry. All to keep him out of Hogwarts, so Riddle's memory couldn't harm him.
Clemael, one of the protagonists of Hand of Mercy. The plan to undo all the evil in the world isn't bad, exactly, but Clem isn't bothered that this will destroy all of linear time.
The Birds of Prey from The Princess 99 commit brutal murders against wizards through the entire book. But then you consider that they are trying to give Nons (non-magical people) civil rights in a world that considers them lower than animals. This doesn't excuse what they did to Axel.
Grand AdmiralThrawn really just wants to protect the galaxy (and his people in particular) from all threats. The problem is that he's an imperial trying to crush the New Republic, and he's not afraid to do some truly villainous things to achieve his goals, like oppressing and enslaving a race, or attempting to kidnap a pregnant Leia so that she and her unborn twins can get mind raped by an insane dark Jedi. He's more pragmatically ruthless than outright evil, and as we find out more about him, he gets more and more morally ambiguous, but by the end of his career, he definitely isn't a good guy.
The novel Outbound Flight shows him as a decent guy whose methods are considered extreme by Chiss standards and their "no first strikes" policy. Then, Palpatine's emissary informs him of an extra-galactic force that threatens the entire galaxy (the Yuuzhan Vong, presumably), forcing Thrawn to become this.
In The Fight for Truth, part of JediApprentice, the rulers of the planet Kegan have prophetic dreams. Trying to prevent them from coming to pass, they completely cut off trade and travel between it and the rest of the galaxy, closely monitor all of their citizens, educate via misleading propaganda, assign jobs to people regardless of personal preferences, and abduct chronically ill or skeptical children to be raised in solitary confinement, sometimes involving "sensory deprivation suits". What are their visions of? The Republic becoming The Empire, stormtroopers marching across Kegan, the planet itself being destroyed. They recognize the harshness of their methods, but believe that they will prevent that from happening.
Abraham Quest and Robur in Stephen Hunt's The Kingdom Beyond the Waves seek to recreate the perfect society that once existed in the form of Camlantis Unfortunately, it requires the destruction of every other society on Earth and their inhabitants.
The sixth book of the Firekeeper saga, Wolf's Blood, introduces Virim, the sorcerer who created the plague that killed all the world's magic users a century ago. His reasons for doing this rested primarily on the fact that his people were prepared to conquer and kill the Royal Beasts who lived in their colony lands.
A post-Columbine Young Adult fiction book called After... features a (presumably) government attempt to quell potentially Ax-Crazy kids that gets increasingly out of hand. "Grief councilors" who tell the protagonist to throw a game to the victimized school (at the last minute, he decides not to) and "suspend" a student for wearing a red ribbon (the shooters wore red, see) that was honoring her brother who died of AIDS gives way to spy cameras in school TVs and hypnotic emails that render most of the parents blind to what's going on. It's only when the first school's entire student body suddenly disappears and rumors of detention camps in the desert where the young prisoners are being killed for attempting to escape start filtering back does the protagonist and his family decide to get out of town.note Mind, this is a very sympathetic remembering of the plot. When I read it, it was so over-the-top that I thought the villains were some kind of cult or rogue operatives who needed a compound full of kids for something. If I recall correctly, it's never stated exactly who the villains are working for.
Any number of characters from The Warlord Chronicles, but Merlin and Nimue are certainly the biggest examples. Eventually, Merlin backs away from the slippery slope. Nimue turns Knight Templar, and is instrumental in destroying Arthur's realm.
In the Dale Brown book Act of War, the eco-terrorist organisation GAMMA is not above doing things like using backpack nukes to attack the big businesses it believes is ruining the environment. Then subverted when it turns out that this was the Deceptive Disciple's plan and the group's leader didn't want it to happen.
Anaria from The Guardians decided that the best way to end a war was to slaughter one of the armies in its entirety. After that, she decided that she was thinking too small and needed to apply her idea to the entire planet, until the only people left alive were the ones who agreed with each other. But don't worry, she'll still respect free will. She'll just make sure that humans have no other options except to choose peace, joy, and love.
The Vampire Files gives us Federal Agent Merrill Adkins (from A Chill in the Blood). He's perfectly willing to gun down bystanders in his pursuit of criminals.
In The Dresden Files, Martin will do anything to destroy the Red Court. He first appears for the purpose of interfering in a duel that may lead to a cessation of hostilities between the Court and the White Council, because they're the most powerful weapon available pointed at the Court, and he's determined that they fire. In Changes, he betrays the Order of St. Giles to gain the Red King's trust, hands Harry's daughter to the Court, and gets Susan to kill him in revenge so that Harry will be forced to kill her and thus obliterate the Court. It worked.
The Big Bad of Summer Knight resorted to trying to create a major power imbalance between the Fae to destroy the world and start it anew, but only because they were tired of the death, destruction, and atrocities caused by the endless cycle, and puts up so amiable an argument that Dresden later calls Aurora a well-intentioned-yet-crazy Fae lord. Subverted in that the main antagonist is Ax-Crazy.
Kimoru, a necromancer traveling around with sinister wizard Cowl in Dead Beat, constantly talks about the benevolent side of her art (like how she kept a dying man alive until paramedics could arrive and fully fix the damage), and says that she wants a world where no one has to deal with the tyranny of death. And if her boss has to pull off a hideous ritual that will result in thousands of deaths and bring him up to the level of a minor god for this perfect world to happen, then so be it.
Alloran from Animorphs, who chose to genocide the Hork-Bajir to weaken their usefulness as the Yeerks' shock troops.
By the end of the series the Andalite military in general seems to be this, since they are convinced that the Yeerks have won Earth and are planning to do the same thing again.
Paul Bowman from the Council Wars series has some points about the current state of humanity that his opponents agree with, but they disagree with the conclusions he's drawn and rather violently disagree with the methods and allies who've lined up with him.
At least at first, Stannis doesn't seem to truly buy into Melisandre's religious beliefs, and admits that he's merely letting her spread her message because her supernatural powers are useful to him. In fact, he comes across as one of the few true atheists in the series. It's arguable whether or not that changes later on.
Either way, Stannis is a Well-Intentioned Extremist in a different kind of way. He's fanatically devoted to his own unique notion of justice: to him, all good deeds must be rewarded, and all evil ones punished, even if they're committed by the same person. One person comments that if Vargo Hoat had been on Stannis' side, Stannis would've given him a lordship for his assistance right before hanging him for his crimes. He's also unflinchingly stubborn, to a point that even he admits that it's a fault of his. These traits lead him to launch a war (and ally himself with Melisandre despite his many misgivings about her) for the throne of Westeros, even though he doesn't even want to be king and admits that he wouldn't be well-suited for the task, simply because he knows that it's rightfully his. In his eyes, it'd be selfish and unjust if he didn't try to win the crown.
Prince Kieran in Salamander is an Anti Villain variant. Also unusual because he switched to the heroes' side when extremism became no longer necessary.
Safehold provides a protagonist version of this with Merlin Athrawes. His primary goal is to bring humanity out of its enforced Medieval Stasis so they can fight and defeat the aliens that nearly exterminated them hundreds of years ago. However, to accomplish this, Merlin must provoke a religious war already in the making and topple the Corrupt Church that currently rules the world, a war Merlin knows will kill tens of thousands at least, many of them innocent.
One of the series' antagonists, Zhaspahr Clyntahn, is especially dangerous because he has himself convinced that he's merely this.
Jacen Solo's reasons behind his turn to the Dark Side of the Force was because of this trope as well as a Papa Wolf: He saw into the future and saw his daughter, Allana, standing next to Darth Krayt, who was sitting on the Throne of Balance, and became such as a desperate measure to ensure that future did not come to pass, certainly not Allana being aligned with Krayt at least.
In Poul Anderson's "A World Called Maanerek", Korul Wanen is so loyal to the Cadre that he is pleased that he was dumped, with no memory, on a planet to see what would happen, despite the risk to his life.
In James White's novel Under Kill groups of well-intentioned extremists keep causing atrocities in a near-future energy-poor Earth, adding to the problems of what is already a Crapsack World.
The woman who attacked Ben and Dr. Sacreya in Sacreya's Legacy believes zombies are monsters that should be destroyed and that Sacreya is a mad scientist who needs to be stopped, neither of which is a hard conclusion to sympathize with, given what happens to Vogan Point. To her, even a thinking, reasoning zombie needs to be destroyed.
Trapped on Draconica: This is Gothon's opinion of himself: lives lost in his conquest will be offset by lives saved afterward. Ben tells him that another guy in Earth History tried the same thing and is remembered as 'one of the biggest bastards in history'.
In Vernor Vinge's Rainbows End, Albert Vaz has created a Mind Control virus because he sincerely believes it's the only way to keep the world safe, when even terrorists and cults can afford nukes and deadly viruses.
Skulduggery Pleasant has Eliza Scorn and Argeddion, who are both affably evil characters, or argubly not evil at all, just crazed/obsessive.
Luke Castellan from Percy Jackson and the Olympians could qualify, as he genuinely believes (and perhaps could even have a point) that the gods are selfish and evil.
The Anarchist from Clockwork Angels resorts to violently disrupting the public (often resulting in death) to "wake them up" from the tyranny that is the Watchmaker. The same goes for the Watchmaker, imposing extreme order on the people to protect them from danger.
Adventure Hunters: Ryvas wants to provide for his people and make sure no one dies in war ever again. His solution is to break the Nuclear Weapons Taboo and replace human soldiers with golems.
The Mortal Instruments: Valentine. Unfortunately, his plan to reform the Clave to protect against demonic threats involves raising a massive demon army and slaughtering them all.
Captain Nemo, the Anti-Hero who first appears in Twenty Thousand Leagues Under the Sea, can be said to have had genuine good intentions that made him a sympathetic character. The deaths of his family gave him a hatred of oppressive governments (especially imperialism) and a genuine concern for innocent life. Still, as one character put it, it was not his right to judge nations the way he did, via the vigilante actions he took to punish them for what he saw as injustice.
Deconstructed by the Apostle Paul in Romans chapter 3 in The Bible. As he writes in Romans 3:8 (NKJV), "And why not say, 'Let us do evil that good may come'? - as we are slanderously reported and as some affirm that we say. Their condemnation is just."
"Skip" Wilson, newspaper columnist turned eco-terrorist in Carl Hiaasen's Tourist Season. He deplores the destruction of Florida's environment by the flood of development and tourism. His solution? Destroy the tourism industry and collapse the economy through murder, bombings and kidnapping.
The Christian fundamentalists in control of the American government in Christian Nation want to prepare the nation for the Second Coming of Christ...so to that end, they strip away all Constitutional rights for the citizens and install a Big Brother-ish theocracy where God's law is the law of the land.
The Ukiah Oregon series has The Pack, although some cross over into Knight Templar territory. They are a band of outlaw bikers who routinely commit murder, theft, arson, and a myriad of other crimes in their endless war against insidious alien invaders. This is still the good outcome.