The Circles from the Deva Series. They firmly believe that artificial magery will lead to The End of the World as We Know It and seek to kill Hayate and friends for using Devices. Admittedly, there is a smidge of truth in their beliefs, but the extents to which they go, combined with their insistence on refusing Hayate's offers, do not help their case.
Talon Ryashen, the "Fairy Tale killer." He was turned into a Super Soldier by Fairy Tale, and is now on a Roaring Rampage of Revenge against anyone who was ever a part of the organization. It doesn't matter if said members defected, were Locked Out of the Loop, or non-combatants; if they were even remotely a part of Fairy Tale, they're on his hit list. Case in point: despite knowing that Dark left Fairy Tale a long time ago and is one of the heroes who slew Alucard, Talon flat-out states that he doesn't care; all that matters is that Dark was a member of Fairy Tale, and thus is irredeemably evil in his eyes.
Fairy Tale themselves. For all of their claims on monster equality, they're more focused on anti-human extremism to the point that any monster who even thinks of siding with humanity is automatically the enemy; they have personally destroyed Ahakon's hometown for refusing to side with them, and tried to do the same to Mizore's hometown twice, on top of attempting to destroy Yokai Academy for teaching coexistence. In fact, in Act VI chapter 52, after seeing Moka preach human/monster coexistence on national television, both Gairen and Raika openly state that they're beginning to see why Gyokuro hates Moka so much.
The HDA is this throughout Act V and most of Act VI, given their Aggressive Categorism of all monsters as evil beasts. In Act V chapter 23, Marin explicitly describes their treatment of monsters as inhuman, and in Act VI chapter 25, Moka outright declares them to be nothing but a barrier in any efforts to attempt peace between humans and monsters, since they, in her words, "treat all monsters as absolute evils regardless of their nature." As of the end of Act VI, they've finally grown out of this, in part due to a Reasonable Authority Figure in their new director, Hothorne Tamaka.
Subverted in the Sonic the Hedgehog and Sailor Moon crossover Chaos Infinity. Chessmaster/Mad Scientist Dr. Eggman manipulates the Sailor Scouts into thinking that Sonic and his friends are the ones responsible for the crisis in Tokyo and pushes them to fight each other, thinking that the Scouts are too much for his archenemies to handle. His plan fails when Sonic gathers enough Heroic Resolve to pull out his own Chaos Blast to overpower their rivals and calls out BOTH the Sailor Scouts and the people of Tokyo for their mistreatment. And then Eggman nearly kills Sailor Moon when using her and the Master Emerald as batteries for another one of his war machines to take out Sonic for good and everyone knew from then on who was really friend and foe. Again, it backfires. After stopping his final weapon, the Sailor Scouts and the Freedom Fighters become friends.
In the Sonic the Hedgehog fanfic Prison Island Break, Silver is the nicer kind of Knight. However he is always convinced that he is morally in the right, despite also being a murderer. His greatest fear is becoming his father.
In the Pony POV Series, one of the Alternate Universes that Applejack sees at one point is a world were the Mane Cast have become a group of dictators who brainwash and otherwise brutally suppress anything "disharmonic". They are actually based off of the Justice Lords from the Justice League series.
Subverted in Cheerilee's Garden. Cheerilee justifies her many brutal murders by claiming that she's doing the world a favor by ridding it of degenerates and corrupting influences ("weeds"), but just in case the reader wasn't already tipped off by her obvious eagerness and pleasure in committing such acts, Twilight flat-out states in the third chapter that Cheerilee is nothing more than a HedonisticSerial Killer.
The Law Heroine in Goddess Reborn Chronicle, whose soul was bonded to an angel-until she finds herself better treated by enemies than allies, questioning her own faith and motivations.
In Touhou canon, Yukari Yakumo is usually portrayed as the overseer of Gensokyo, when working being a Trickster Mentor to Reimu and tending the Hakurei Border. However, when the fic oges Darker and Edgier, Yukari will usually be a ruthless knight templar, that measures no consequences in order to keep the barrier up and Gensokyo safe. This goes from hunting Rin, provoking a small war with Yuuka and nearly executing Remilia for her failure in Imperfect Metamorphosis or spiriting away selfish kids to destroy the balance of Gensokyo in order to keep the place busy and prolong its lifespan in Diamond in the Rough (Touhou).
This is Danzo's portrayal in Vapors. He is a cruel and ruthless monster, but he's a cruel and ruthless monster for the betterment of Konoha, and even Aiko, who despises him, agrees with some of his ideas. When he is waiting to be executed for treason by his own home, he refuses to let a Root operative spirit him o safety, instead only asking that the explosive seal on his chest be defused before he dies, so that Konoha won't suffer any collateral damage.
A common trope in Sonic X: Dark Chaos, particularly among the Angels and the more-fanatical Demons. The Muslims and the Emirate of Mecca take this trope Up to Eleven. Cosmo's mother Hertia also eventually became this, torturing Tsali's sister and killing a recently born Seedrian male child because of Daffodil's religious influence.
Celestia is stated to have become Corona because of centuries upon centuries of stress from trying to keep her little ponies safe in a world full of threats. Eventually she snapped, trying to destroy every possible threat and rule every last detail of every pony's life so as to ensure that they could never get hurt again. Even in the present day, she genuinely wishes the best for Equestria, she simply is totally deluded about what that is.
Duke Fisher seeks to take over the Night Court because he believes that only his constant vigilance protects Equestria from the surrounding nations and from Corona's wrath.
Twilight Sparkle's brief descent into villainy originated in a genuine belief that she would make a better Element of Magic than Trixie, and a relentless determination to prove herself right.
Applejack likewise is constantly trying to acquire more land, bits, and resources not out of greed, but because she genuinely believes that the Apple Trust is perpetually on the verge of going bankrupt and that if it does go under, all Equestria will starve.
The Jackie Chan Adventures/W.I.T.C.H. crossover fic Kage has Kur, one of the leaders of the Meridian Rebellion. He harbors an unsettlingly extreme hatred toward the shapeshifter race, expressing a belief that their annihilation is in Meridian's best interests as much as Prince Phobos' demise. He led a pogrom during Phobos' rule, capturing and killing many shapeshifters, including children and ordinary people who simply birthed them, like Miranda's parents. Now he's plotting from the sidelines to gain Queen Elyon's support for a much larger pogrom...
The villains of The Death Of Princess Luna turn out to be several members of the royal guard who have thoroughly deluded themselves into believing that they're only doing the right thing by kidnapping Princess Luna, manipulating the entire kingdom into believing her to have died and keeping her inhumanely imprisoned in order to kill her at the right time on some screwed up belief that it's necessary to permanently destroy Nightmare Moon so that she wouldn't possess some other pony's body and kill them in the process (like they believe to have happened to Luna).
One Wish For Nothing: Stronghold Halfdragon, a member of a pony-dragon hybrid race called the Draekin, is the leader of a cult called the Order of the White Dragon. A thousand years prior to the story, she waged a fierce war against Equestria, but was supposedly defeated. In reality, she had actually killed Celestia and taken her place for the next thousand years.