Captain Nemo, the Anti-Hero who first appears in 20,000 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.
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.
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.
A post-Columbine Young Adult fiction book called After... features a (presumably) government attempt to quell potentially Axe-Crazy kids that gets increasingly out of hand. "Grief counselors" 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.
General Sarov from Skeleton Key wants to use a nuke to make it look like 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 drug 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.
Nita from Allegiant. She wants to stop the Bureau from further discriminating against the genetically damaged like herself (especially when the reader finds out how extreme they, or rather just David, go to uphold it), though her method to do it isn't nice to say the least. She even designs a bomb with Four which indirectly causes Uriah's brain damage and eventual death.
In All Our Yesterdays, James wanted to use time travel to save people from dying, but he ended up using it to kill people who became a threat to him, including his own brother, and turned everything into a police state.
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.
Rachel, though going down many morally dubious paths, consciously never falls into this. She even laughs bitterly when she hears the words 'We have to win'.
Rachel: Even I know those are the first four words to hell.
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."
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.
Subverted in The Chathrand Voyages. Arunis - arguably the most dangerous of the series Big-Bad Ensemble - claims at one point that the he's just trying to unify the world under his control for the benefit of mankind when trying to talk Pazel onto his side. Pazel doesn't buy it, pointing out that Arunis's methods are so horrific that he can't imagine any potential good would outweigh them, and he's rightnote Keep in mind that Pazel's home city-state was brutally occupied by the neighboring empire in the name of "protection", so he's quite familiar with just how hollow a nebulous "greater good" sounds to the people who get stepped on along the way. Arunis doesn't give a damn about the world, and in fact is trying to wipe out humanity in order to convince the local Gods of Evil to elevate him as their newest member. The Well-Intentioned Extremist bit was all lies.
The CHERUB Series' most prominent villain is arguably the eco-terrorist organization Help Earth.
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 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.
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.
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.
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). Spectacularly averted in the original trilogy, however, where all the villains were selfish and power-hungry Card-Carrying Villain types.
In the Dreamblood Duology, Eninket doesn't actually want to live forever and wage war until the world is united under his rule, he just sees it as the only way peace is actually possible. He could also just be really, really crazy, but the people who knew him best stick with this one.
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 Axe-Crazy.
Kumori, 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.
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 Fellowship 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.
Gatt Coulomb is an assassin for the criminal organisation Père Noël- and sincerely believes that everything he does is necessary in order to "correct" the world.
As the leader of the Tasan Party, Gammon Octo firmly believes that the ends justify the means when it comes to bringing an end to the corruption and suffering in Levianta and Elphegort. Later, he seems to reject that mindset, even condemning it in his commentary on the Red Shoe Parade. Still, he works to destroy the sin contractors after the world ends, in order to to save the rest of the world.
Vicar Brusander of The Emigrants is a difficult character to like from a modern point of view, when he becomes the mastermind behind a prosecution of Danjel's harmless religious movement. But at this point in Swedish history, dissenting from the established Lutheran church is still against the law. And the vicar hardly is the only person in the parish, who has become suspicious of just what Danjel might be up to. Furthermore, it seems like the vicar also feels that punishing Danjel and his followers is for the best of the people. His belief is that if everybody was allowed to choose their own faith, society would be plunged into chaos. So even though the story puts most of the sympathy with the dissenters, Vicar Brusander is still portrayed as this trope rather than as some selfish one-dimensional villain.
Empire Star by Samuel R. Delany has the members of the Geodesic Survey, who are trying to compile an encyclopedia of everything. (They're up to volume one hundred and seventy six: Bba to Bbab.) They'll do literally anything to get more information for their encyclopedia; even kill. In fact, a little murder might help them get a jump start on the chapters which cover Biology, Human.
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.
The clergy of the God of Death and the Dead in Jean-Philippe Jaworski's Gagner la Guerre (To Win the War). The last king of the huge Leomance Kingdom entrusted them his will ( part of their function ) that his unborn child, if a son, should reign after him. Regrettably, he was born a feeble-minded cripple and civil war soon enough tore the kingdom apart. The priests attempted to hold it together, supplementing the meagre loyalist forces with massive Death magic and an alliance with orcs. It didn't end well for anybody concerned.
In The Goblin Emperor, one of the men responsible for the death of Maia's father and half-brothers is a kind of communist who wants to change things for the better, and says that he already succeeded because Maia is a much better emperor than his father was or his brothers would ever have been. Maia, who indeed is very kind and compassionate, doesn't know what to reply because the man is right, even though Maia doesn't agree with his methods.
Vanessa, of the Goosebumps book Chicken Chicken, just wants kids to learn manners. Unfortunately, her methods make her one of the most hated villains in the series.
Subverted or deconstructed. Vanessa's so called "good-intentions" only highlight how despicable she is, since not only does she transform children into Body Horror abominations, but she has the gall to act like this is an acceptable treatment for naughty kids. In any case, the fact that Vanessa sees nothing wrong with these actions makes her one of the most disgusting, hypocritical villains in the entire series.
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.
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 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.
In The Hearts We Sold, the Daemon's intentions are noble, since he's trying to stop the world from being destroyed, but his methods endanger his charges, all of whom are hapless but relatively innocent teenagers. It works, but at least two people wind up dead.
The Hero Is Overpowered But Overly Cautious: The residents of the Dragons' Den want to sacrifice Elulu to create the holy sword Igzasion, all to defeat Gaeabrande's Demon Lord. They'll go as far as to slip the party paralytic drugs to ensure that they can't interfere with the ritual. They also killed any of their citizens who opposed the sacrifice, including Elulu and Mash's families.
Lord Asriel from His Dark Materials. His goal is to eliminate an evil god, but the ways he gets to it includes killing a little boy by separating him from his soul.
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.
Tam Lin in House of the Scorpion attempted to assassinate the prime minister of an unknown country, presumably the United Kingdom, 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.
The Hunger Games: President Alma Coin claims to be one, and goes to very extreme measures, like having children killed, so that she can overthrow the Capitol.
Edgar Geist of Humane Tyranny believes that the Earth would be better off if the human race went extinct. Ironically, he still deeply cares about his partner, Harvey, and his protege Ray, and never actually kills anyone at all during the novel's events.
Journey to Chaos: During his Motive Rant, Duke Selen Esrah calls Princess Kasile a poor excuse for a future queen because of her arrogance and paranoia. He believes that taking the throne from her is for the good of Ataidar. To this end he allowed monsters into the city, framed her for treason and launched a coup.
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.
Killer Species: Series villain Dr. Catalyst starts as a highly egotistical one, creating hybrid super-predators for the purpose of hunting and destroying invasive species in Florida, thereby protecting the native species and reversing the ecological harm they do, and doesn't get why people see he and his creations as the bigger threat - he also made them controllable and unable to breed (though some of them eventually adapted to overcome this) so they wouldn't take their targets' place as a threat. In books 3 and 4, he abandons this and just decides to kill off a lot of people for opposing him.
Valentine Morgenstern from The Mortal Instruments. Unfortunately, his plan to reform the Clave to protect against demonic threats involves raising a massive demon army and slaughtering them all.
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.
In Skeleton Coast, a super environmentalist plans to combine a toxic oil spill with a super-hurricane to hit Florida, believing this will be the wake-up call to the public to change their ways on pollution. In a final battle, hero Juan Cabrillo points out how the man could have used the billions of dollars he wasted on this scheme for something a lot more effective.
Juan: That's the problem with people like you. You're about propaganda and press releases, not concrete solutions. People don't respond to ultimatums, only alternatives.
In Plague Ship, the main villain claims he is doing humanity a favor with his scheme to render half the human race sterile. He truly believes in future generations, he'll be revered for preventing the "inevitable" collapse of humanity. Again, Juan points out how full of crap he is... particularly because the man was a Nazi scientist at Auschwitz.
The Dirk Pitt adventure Celtic Empire has industralist Evanna McGee concluding that men have made a mess of the world. She thus plans to release a virus that will destroy any embryo with a Y chromosome inside it so only females are born. This would mean that within a few generations, no men are left on Earth with cloned embryos ensuring a female race survives. Pitt openly lampshades that the troubling part of this is that McGee A) truly thinks greed, violence and stupidity are only male traits; and B) that every other woman on Earth will be perfectly happy to go along with this mass gendercide.
The furry novel Otters in Space makes this a slightly odd Zig-Zagging Trope as more of the antagonist's intentions are revealed. In this universe, cats are the victims of Fantastic Racism. The villain, a cat, is willing to have the protagonist killed because she knows too much about her plans, and appears to have had someone disappeared before. But she was actually working with the disappeared employee, and covering for her so they can stay in business together. But that business is embezzlement and smuggling people. But they're actually sending them to an Underground Railroad colony on Mars. But the colony is full of also-racist for-profit jerks. But the villain was trying to protect the entire planet full of people by sending them the money she was embezzling. In the end, she just ends up taking the fall and being arrested for corruption, while the colony might have to reconsider its admissions standards.
Johannes Lillegard in Pact is a sorcerer who maintains a large area of a Canadian town where he's created copies of the inhabitants, whose suffering he auctions off to various supernatural creatures. His justification for this is that, firstly, while they're hurting copies they aren't preying upon actual humans, and secondly that by charging for the privilege and thus gaining great power he's hoping to set an example for other practitioners, who can do the same in their territories, thus preventing the supernatural creatures from lashing out at the rest of humanity out of frustration.
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.
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.
He definitely has a point. The gods are selfish and most of them don't care about their children or even each other. Even Percy thinks he has a point, and he hates Luke with a passion for the majority of the series. Unfortunately, Luke's methods include siding with a Titan that's much worse than the gods, and the war he helps start results in many demigod deaths. (Although it's debatable as to whether or not Luke was completely in control of himself; remember, Kronos was able to manipulate an actual god before Olympus even knew he was back.)
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.
Mrs. Beeson in The Prophet of Yonwood, who strictly enforces her interpretations of Althea's delusional mutterings because she believes that they are instructions from God, telling the world what they must do to be free of sin.
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.
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."
In The R Document by Irving Wallace, Attorney General Chris Collins supports the 35th Amendment which would give the FBI more power to handle growing crime in the United States. The 35th is being pushed by Vernon Tynan, head of the FBI. But with some allies, Chris discovers that as soon as the 35th is passed, Tynan will push through the R Document (as in "reconstruction") which will suspend the Bill of Rights and allow martial law to rule over the nation. At first, Collins believes Tynan is being driven by the power he would get as the head of new law enforcement. However, Collins soon comes to more chilling conclusion that Tynan truly believes the only way to "save" the country is to turn America into a police state.
In The Reader (2016), the Guard wants peace in Kelanna, but that involves keeping vital information from the common populace, kidnapping boys and turning them into killers, raiding the ships of several kingdoms, and brainwashing prisoners.
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.
Merlin Athrawes provides a protagonist version of this. 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. He can and will order any atrocity he feels is necessary, such as a method of execution consisting of long, drawn out, and public Cold-Blooded Torture, all the while espousing that it is in the defense of God and Mother Church. Multiple characters note that he seems to sincerely believe this, but at the same time he consistently demonstrates that what he claims is Mother Church's and God's will just so happens to also be his will, and he would rather drag the Church with him into defeat than pursue anything like a reasonable diplomatic solution.
Eric Langhorne and Adorée Bédard, who were responsible for setting up the Path of Inspiration keeping Safehold in Medieval Stasis, genuinely believed it was the best way to save humanity permanently from extinction, due to being utterly traumatized by the war humanity was losing against the Gbaba.
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.
Prince Kieran in Salamander is an Anti-Villain variant. Also unusual because he switched to the heroes' side when extremism was no longer necessary.
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.
In the Spaceforce books, Ashlennï¿½s 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 Taysansï¿½ technological advantages. Jay admits that he's probably right, then summarily executes him anyway.
Thrawn ends up here by the time of his last campaign. He started out as a morally ambiguous character in Outbound Flight, but turned into a ruthless, pragmatic man who wasn't above committing some truly villainous acts to achieve his goals. His motives were understandable, especially after they were retconned into stemming from a desire to protect the galaxy from an imminent invasion, but he was most definitely not a good or nice man. His men adored him, but Leia might have had something to say about that.
In The Fight for Truth, part of Jedi Apprentice, 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.
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.
Superheroes Anonymous has an entire medical disorder, Villain Syndrome, for this trope. Regular villains are out for money, or to create destruction. Victims of Villain Syndrome are convinced that they need to fix the world by any means, and the problems they see include people being unable to enjoy pain or the lack of ability for the common man to photosynthesize.
In The Testament Of Jessie Lamb the Mother Death Syndrome, a disease that kills all pregnant women even before giving birth, causes people to panic, and there are several extremist camps. There are those who believe it's the revenge of nature, and the solution is to stop experimentation on animals. There are the religious extremists, who think it's a punishment of God, and there is FLAME, an extremist feminist group who suspect that the disease is men's newest weapon in the war against women. Jessie sympathizes with the animal rights group, thinks the religious extremists are weird, and at one point lies to FLAME protestors, because they don't want her to sacrifice her life to give birth to a baby. (FLAME wants to wait for science to find a solution that requires no more women to die, but Jessie wants to make her sacrifice before she's too old, as only girls under sixteen qualify for the vaccinated frozen fetus implantation program.) The FLAME protestors are rather peaceful, and actually protected scientific laboratories against the other groups (who either think science is sinful or is against animal experiments). They let Jessie pass after she tells them she only wants to visit her father, who works there, while she's in fact intending to talk to the scientists who could implant an embryo into her womb, thus killing her.
Kramer from TimeRiders, who attempted to avert the horrific wars and environmental damage caused in the latter days of the 21st century, through the use of time travel to create an empire using the forces of Nazi Germany.
"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.
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".
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.
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.
Victor Dashkov from Vampire Academy really does want what is best for the Moroi. He just does not care who he sacrifices to accomplish his goals.
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.
Most of the villains in Victoria are this to some degree; even the neo-Nazi faction gets a somewhat sympathetic take this way, presented as a semi-understandable (over-)reaction by "Law and Order" types to years of chaos and disaster in a dystopian future. While the story has a few straight Card Carrying Villains as well, it emphasizes that most of the bad guys view themselves as good guys and have at least some kind of sympathetic core to their motives—Even if they often go very much too far in implementing them.
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 Witchlands, Vivia turns to piracy despite the damage this might bring to the Twenty-Year Truce and Nubrevna's reputation because her people need to eat, no matter where the food comes from.
In Worm, Accord became a villain in order to implement his plan to end world hunger.
Most everyone in Worm is some stripe of this, up to and including the protagonist. The tagline is "Doing the wrong thing for the right reasons."
Cauldron is an organization that regularly performs human experimentation and brainwashing on prisoners, secretly run the Protectorate, and have accidentally spawned horrible monsters that have killed millions of people, all to save the world from Scion. It turns out that their brilliant plan was to wait for Scion to start killing people and then attack him with an army of capes, which fails so badly that the apocalypse gets worse as a result.