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  • Old World of Darkness
    • The Garou from White Wolf's Werewolf: The Apocalypse. Each of the Changing Breeds was created to serve Gaia, and the Garou served as her warriors, protecting her from all things "of the Wyrm." Unfortunately, the Garou thought they were in a position to tell the other Breeds how to do their jobs. On top of that, Gaia never told them about some of the Breeds, or even some of the other tribes of Garou. Genocide ensued. By the time the game begins, three Changing Breeds and one whole tribe of Garou have been driven to extinction, the other Changing-Breeds are mostly in hiding, and the Garou have finally come to realize just how much they shot themselves in the foot. Furthermore, while most of the tribes have valid motivations, some of them go much, much too far. Don't ask about Red Talon "Christmas trees."

      To be fair to the Garou, they were doomed from the start since the Triat, the uber-gods who embody the cycle of Creation, Stasis, and Destruction, are all completely screwed up. Instead of the Wyld creating, the Weaver defining, and the Wyrm destroying (the natural order of things), the Weaver went crazy and captured the Wyrm in a web, making the Wyrm go completely out of control. The Wyld, the only one of the Triat that might be on the Garou's side, is still attending to its duties; trouble is, due to its nature, it's not exactly sane. The Garou have several other gods on their side, including Gaia, the spirit of the planet itself, and Luna, the spirit of the moon, but it's unlikely to be enough. They're fighting to protect a system that is doomed from the get-go.
    • The Technocracy from Mage: The Ascension is an organization dedicated to making the world safe and predictable for sleepers. Unfortunately, their plan includes genocidally exterminating all supernatural creatures they find, even those who are also trying to protect the helpless and innocent, as well as attempting to monopolize scientific research and advancement, and lying to the sleepers about the true nature of reality.

      But from their point of view the supernatural creatures include parasitic bloodsuckers that seek to control all society in their games, genocidal furry monsters that want to return humanity to Stone Age population levels, and dream parasites that latch onto people and use them as hosts.
    • And on the other side, you have the Euthanatos, a Tradition dedicated to doing to the population what a gardener does to weeds. They try not to jump off the slippery slope, but...
  • Mage: The Awakening
    • This essentially defines the Banishers. They believe the supernatural, especially mages, to be inherently evil (not necessarily without reason). Their solution is to attempt to wipe out every single supernatural being (especially mages) that they come across. Banisher Mages see the entire cosmology as they Awaken (including the Abyss) and how it all fits together. After that, they decide that they will use magic, but only to ultimately stop it from ever being used again.
    • This is one interpretation of the ancient conspiracy the Seers of the Throne.
    • Also a good description of the Guardians of the Veil. Probably the only Well-Intentioned Extremist group that fully acknowledges that status. It's right there in their creed: "Sins for a just end bring wisdom to the Awakened."
  • WoD Hunters in both Vigil and Reckoning. The average Hunter group has a 75% chance of trying to kill at least one benevolent or neutral supernatural in the name of keeping humanity safe from things that go bump in the night. A fair number of plot hooks in assorted Hunter sourcebooks revolve around overzealous Hunters being tricked into going after the good-guy faction of a given splat by one of the bad-guy factions. They aren't helped by not having access to information about the various supernaturals that could help them sort good from bad.
  • Genius: The Transgression, a fan-made game for New World of Darkness
    • There are the Lemurians, Geniuses who haven't gotten the memo that they literally cheat reality. They think that something Went Horribly Wrong in the past, and that they have to fix it in the present. They range the gamut from Complete Monster Knight Templars to playable Anti Villains.
    • This game, being set in the World of Darkness, has plenty of non-Lemurian Hoffenhungs (those who became Geniuses through a wish to change the world)) who end up becoming this, particularly if their Karma Meter falls too low.
  • Warhammer 40000:
    • The Tau of regularly employ mass murder and orbital bombardment when a species denies multiple "offers" to join them. The "well intentioned" part is what sets them apart from everyone else - factions such as the Imperium will blow up their own planets and murder billions in the name of mere survival.
    • Also in the setting are radical Inquisitors who decide that the best way to defeat the forces of Chaos is to turn Chaos against itself. If they're lucky, they end up executed by their colleagues for heresy. If they're unlucky, they are lost to The Dark Side. And even if Inquisitors are lost to The Dark Side, many of them still try to serve the Imperium, no matter how many innocent lives are lost in their schemes.
    • No mention of the Eldar? They are so devoted to the continuing survival of their species that they are willing to sacrifice everybody else to keep going. One of the sidebar quotes in the Eldar Codex even says, "We would rather ten million humans die than one of our own."
    • Most of the Chaos Space Marines start out this way before the Drop Site Massacres. Some still are. Point goes to Alpha Legion, who only sided with Horus due to them foreseeing that it would ultimately lead to the best possible outcome for the galaxy if Horus actually won. Indeed, they are still loyal to the emperor, although in the darkest way possible.
  • The Lizard Men faction of Warhammer's goals are sympathetic (purging Chaos/Skaven, trying to follow the plans of the Old Ones), but their methods are ruthless.
  • In the Eberron setting for Dungeons and Dragons:
    • The Ashbound druid sect believe in the Power of Nature. Well, they are druids after all. The "extremist" part kicks in when you consider that they believe that the best way to protect nature is to ban all arcane magic, burn down all the cities, and go back to living in mud huts. They can be any alignment (well, any of the Neutral variants at least, being mainly Druids and all), so they feature both the genuinely well-intentioned Neutral Good ecoterrorists and the rather less pleasant Neutral Evil ones who just like watching cities burn.
    • Queen Aurala also fits this. Well Intentioned? Really devoted to her people and wants to help the whole world. Extremist? She will consider every possibility to make her dream possible, including war.
  • Feng Shui
    • The Guiding Hand is a faction of Well Intentioned Extremists who want to drive all foreign influence out of China, their most iconic fighter being Wong Fei Hong. This may seem like a good thing, particularly because of the opium trade and general imperialism that the Western powers engaged in during the 1800s and the suffering it caused among the Chinese people. On the other hand, Quan Lo, the master of the Hand, is very rigid in his ways, and those who do not embrace them are seen as tools to be used or enemies to be destroyed, making him just as much of a tyrant as Gao Zhang from 69 or Bonengel from 2056. Many Hand adherents despise anything Western or modern, particularly guns and other modern weapons. And Quan Lo's prideful crusade may have some bad consequences — critical shifts shown in the Guiding Hand sourcebook Blood of the Valiant include the extremely stagnant Harmonious Kingdom, where everyone is expected to abide by the laws of the land, technology is outlawed, and All Crimes Are Equal (even rude behavior is punished harshly); and the "Crouching Tiger, Mad Max" setting, which is a post-apocalyptic setting ruled by powerful Chi Warlords who rule by the strongest kung fu.
    • In addition, there's the Jammers, who have seen the effects of the Buro's control of chi upon much of the populace of 2056, and have decided that no one deserves to be enslaved like this. To this end, they want to destroy all chi so that humanity can be truly free from its influence. There are just a few problems with this plan. One: the primary sources of chi are the Places Of Power known as Feng Shui sites, which often take the form of places like schools, hospitals, and other places important to a community or where innocent people tend to gather, and these guys don't care one whit if these innocent people are hurt or killed in the process of "liberation". Two: the Jammers haven't given much thought to what will happen to the world once all its Feng Shui sites are blown to smithereens, and considering that chi is reportedly tied to life itself, the consequences of wiping out the world's chi may be quite bad indeed.
  • Exalted
    • The Bronze Faction have managed to royally screw up the Creation in the process of attempting to save it. And yet, their leader, Chejop Kejak, is still convinced that he's doing the right thing, and even now, with everything going straight to hell (possibly literally, if the Yozis get their way), he firmly believes the world is better off without the Solars. He is one of the last who personally remembers just how bad the late First Age actually was, but he should also realize that just Terrestrials and Sidereals cannot hold off the Yozis, Deathlords, and Raksha simultaneously, especially with the Scarlet Empress missing and the Realm Defense Grid offline.
    • Most Sidereals, and many other types of Exalt, tend to end up in this trope eventually. (Then, if the Great Curse addles them badly enough, the "well-intentioned" part falls right off.)
  • Magic the Gathering:
    • This and Knight Templar are White's schtick. From Ravnica alone, we have the white/green Selesnya Conclave, who wants to keep society together at the cost of individuality; the white/black Orzhov Syndicate, who is much the same without the dryads; and the Boros Legion, whose tactic for building a better world is heavy on the "break heads" side of the scale.
    • Perhaps Yawgmoth could also fit into this trope when he was still a human. After all, he considered eugenics and hybridization between man and machine as perfectly justifiable ways to improve life. Then again, he also infected entire races with fatal diseases just to blackmail them over the antidotes, and then let them die anyway For the Lulz.
    • Yawgmoth's archrival Urza would count as an Anti-Hero version. He's still a protagonist, and could even be called the Big Good of his arc, but in his efforts to stop Yawgmoth from taking over Dominaria, he still did such things as start wars, run eugenic programs that produce disposable slaves to be used as soldiers, kill his allies and using their souls to power bombs, and, in one instance, set off an explosion that destroyed a substantial landmass and led to a practical nuclear winter just to kill his corrupted brother. If Yawgmoth wasn't such a Complete Monster and if his victory didn't spell the horrific torture and subjugation of all Dominarians, Urza would be a straight-up villain.
  • In Monsterpocalypse, the Radical factions are said to be this. Empire of the Apes wants to bring harmony back into nature by leveling human cities, but they also protect primitive villages. As for the Terrasaurs, they just find human factories and industrial wastes tasty.