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Abel Nightroad of Trinity Blood is a crusnik, a vampire who hunts and eats other vampires.
Although it is implied (in the anime) by their dialogue that the Crusnik see themselves as another race entirely, they do need the blood of vampires to survive. Abel is the only one of the three who actually makes it a point to hunt vampires. His sister isn't shown to hunt anyone (in fact, she's the empress of the vampires), and Cain doesn't care who he hunts/hurts.
Alucard and his fledgling Seras Victoria from Hellsing. Alucard is an interesting case; he's frequently as bad or worse than the vampires he's hunting (maybe...) and takes far too much glee in killing them, often getting 'creative' in his methods.
The Shikabane Hime of Shikabane Hime are undead girls who hunt and kill other undead.
Similarly, Mana Tatsumiya is also a half-demon who specializes in exorcisms.
Yusuke in YuYu Hakusho ends up being one when it's revealed he has a little demon in him towards the end of the series.
Hiei also qualifies. Ever since he could walk, he's been brutally slaughtering demons left and right, all because he enjoyed killing. Although for a time, his primary motivation was to kill all the ice maidens from his birthplace.
Darcia in Wolf's Rain is a villainous example, hunting the wolves despite being part wolf via a traitorous bloodline.
Both Merry and Engi from Yumekui Merry are nightmares who hunt other nightmares. That said, Merry just sends them back to the dream world, and Engi tries to avoid killing them, letting Merry finish the job when possible.
Natsuno aids in the efforts to stop the vampires infesting Sotoba Village in Shiki, ultimately killing The Dragon and himself in the process.
The Rogue Titan from Attack on Titan, as it attacks other Titans while ignoring the nearby humans. This is because it's actually Eren, on a Roaring Rampage of Revenge after his Voluntary Shape Shifting powers manifested. Armin successfully invokes this trope, convincing the military that Eren can become their trump card in the battle to reclaim first Wall Rose, and eventually Wall Maria from the Titans.
Ymir also becomes this, when her unarmed squad is cornered in a castle tower by a horde of Titans. Word of God confirms her decision to reveal herself and fight is because she's in love with Krista. She gets overhelmed, but luckily the Survey Corps arrives in time to save her.
I think Carl Van Helsing from Crimson Cross counts.
In Tokyo Ghoul:re, the protagonists are part of a newly-formed team of artificial One-Eyed Ghouls that CCG has created to hunt Ghouls. They clearly think of themselves as still being human, but wield the same abilities as an ordinary Ghoul and are viewed with mistrust by their peers.
Blade is a Dhampir vampire hunter. Him being part vampire, the thing he hates the most has caused him no small amount of grief.
UltimateMorbius is a true vampire and Vlad the Impaler's brother. It is implied that he was the inspiration for Bram Stoker's Dracula.
If you want a not-so-sunny example of this trope, look at Lobo. He hunted down and killed every single member of his own race...for fun.
X-Factor began as a team that hunted down mutants. The general public didn't know that the team members were mutants themselves and that they were actually trying to help the mutants they "hunt" down.
The X-men in general fight evil mutants quite often when they aren't fighting anti-mutant racists.
Would you believe that Sentinels are mutants themselves? Seriously, some people who build them (like Sebastian Shaw) have tried to put a failsafe program into them to use in case they go rogue, which reveals that, since their abilities were "inherited" and improved upon from from the original Mach-1 Sentinels, they are technically mutants. In theory, this would act as a Logic Bomb, causing a rogue Sentinel who has this revelation thrust upon it to destroy itself, as its directive is to destroy mutants. However, this idea hasn't had as much success as whoever thought it up had hoped.
Venom was like this. One of the few reasons he'd willingly ally himself with Spider-Man was to fight Carnage or another Symbiote; he simply hated them. This became a far-more prominent goal when he later became Anti-Venom.
In fact, this seems to be a trait of Symbiotes in general. The one time Venom and Carnage were ever willing to cooperate with each other was to fight a more powerful Symbiote that had been spawned from Carnage's Symbiote.
Many a Mary Sue Hunter can fall into this by accident - one of the main criticisms of the genre (beyond "WHY DID YOU KILL MY CHARACTER I HATE YOU") is that said Hunters often end up being Mary Sues themselves.
If you think about it having a character beat an over-idealized character as such a Mary Sue (with the exception of Anti Sues) has a high probability of accidentally becoming one him-or-her-self because having beaten an over-powered character requires you to be even more powerful or extremely lucky. A way to around this can be to have them have a hard time at first and work hard to defeat the Mary Sue(s) or Marty Stu(s) & then succeed.
According to one version of Blade Runner, the main character who hunts rogue androids is an android himself. If true, this is a rather dark spin on the trope. Basically, androids are detected by being tested for moral feelings and reveal themselves to be amoral. As the androids turn out to be "tin men", this would mean that he is actually worse than his targets. The amorality is explained as resulting from lacking real childhoods and formative years of experience. There is at least one android in the film (two if you count the main character) who has/have memory implants of growing up with a family and loved ones (even if those loved ones died or left). They both show that they have a sense of right and wrong and the definite android is only exposed after hundreds of times more testing than any previous android.
Hellboy is a demon who fights other demons and supernatural monsters. Sometimes, the creatures he fights accuse him of betraying his kind, but he seems to be more worried about becoming like them.
Hellboy II: The Golden Army uses this in the opposite manner from the comic books—to make the monsters that HB fights more sympathetic and to make HB resign from the BPRD.
Notably, in the first movie, he attempts to negotiate with the demon Sammael before resorting to violence.
Night Watch. Both Light and Dark Others persecute their kindred who break the Treaty and threaten to disrupt the Balance between Light and Darkness. Also invoked in that in order to hunt down renegade vampires, Night Watchers need to tune in to the "Call" they use to attract victims. It is only audiable to other vampires, so the Watchers undergo a special ritual that nearly turns them into a vampire.
The protagonist of Richard Morgan’s “Black Man” (“Thirteen “ in the U.S.) is a pretty good example of this.
The White Council and its Wardens in The Dresden Files have distinct shades of this. While wizards aren't considered inherently evil (after all, the Council is itself a wizardly organization), breaking the Laws of Magic even once carries a death penalty and ignorance of said Laws is not considered an excuse. Of course, at least according to the Council Lawbreaking is a highly slippery slope that is easy to jump off of...
The title character of Angel is a vampire who hunts other vampires, and the character Spike also fits this description. When Angel first meets Buffy in Buffy the Vampire Slayer he tells her that what he wants is to kill them, to kill them all. It turns out that he wants to kill them to make up for his own monstrous actions.
Spike initially inverts some parts of the trope since he starts out fighting vampires and demons not because he wanted to be good, but because he could no longer attack humans and REALLY missed violence.
Angel's Dhampyr son Connor takes this and runs with it. Not only did his adoptive father teach him to fight vampires and demons, he groomed him to fight his biological father.
In Kamen Rider OOO, Eiji does not start this way, but he slowly becomes a Greeed near the climax of the series.
In Kamen Rider Wizard, It's double-subverted with the Dragon Phantom. Haruto (Kamen Rider Wizard) summons it to fight against unreleased phantoms, but still need to control it in order to do so. Afterwards, though, the phantom decided to lend Haruto its own power.
Eric Cord from Werewolf did this for the entire series.
Ruby on Supernatural is a demon who fights other demons and helps Sam fight them. Sam is arguably another example of this trope, because his Psychic Powers are caused by having been fed demon blood. Of course, it turns out Ruby is among the worst of the lot and was driving Sam to his destiny to release Lucifer from his prison. Which he did.
In The Sarah Connor Chronicles, Cameron is frequently tasked with hunting and destroying other Terminators. Most often, she does this to protect others, but one episode involves her going into full-on detective mode to track down a Terminator she discovers entirely by accident, and then destroying it.
In the music video for the song A Little Less Sixteen Candles, A Little More Touch Me by Falloutboy, the bassist Pete Wentz is a vampire while the rest of the band are humans who all hunt vampires.
Martin DeVries of Shadowrun deliberately became a vampire in order to hunt them on their own terms.
One of the potential racial backgrounds for the Shardmind in D&D 4e is Shard Slayer, a Shardmind which believes that, since their kind was born from shards of the living gate, then a dead Shardmind's life force returns to it and mends the gaps that allows the influence of the Far Realm to seep through. This mentality is taken to a logical extreme as Shard Slayers hunt down and kill other Shardmind and destroy unawakened shards in the hopes of closing the gate back up.
The Ranger class has the Favored Enemy ability, where the character chooses one or more species and gains several benefits fighting that species. Only an evil Ranger can choose their own species, however, in which case they qualify for this trope.
In Van Richten's Guide to Witches (an accessory for the Ravenloft campaign), the good doctor claims that he wrote the book with the help of a greenhag who despised other members of her species and was all to willing to aid him in publishing a book that could be used against them. (Why? According to Van Richten, she refused to say.)
Vampire: The Requiem has VII, a mysterious group of Kindred who, for some unknowable reason, kill other vampires. Their minds can't be read and they can't be interrogated. Most vampires regard them as an urban legend; however, they do have a book that offers three possible backstories.
Mage: The Awakening has Banishers, mages whose Awakenings went horribly, horribly wrong. As a result, they view magic as something filthy and wrong with the world (they can't use it without feeling innate revulsion) and spend most of their time hunting down other Awakened and killing them to try and "heal" the world in their own way.
Hunter: The Vigil has the Lucifuge, a conspiracy made up of those who believe they carry the blood of Hell in their veins. They spend their days fighting against demons, their brethren who went over to the side of the Devil, and things darker still.
Alucard from Castlevania definitely counts, being heavily inspired by D.
Full-blooded demon Sparda in the Devil May Cry back story turned against his fellow demons and sealed them in their own world. His son Dante, a half-demon himself, carries on by hunting demons who sneak into our world. Nero in DMC4 counts as well, if one accepts the cut material where he is Vergil's son - Dante's nephew - and thus making him a quarter-demon.
The Prinny Extermination Squad in A Promise Unforgotten. They were supposed to be prinnies themselves, but there were too few skins to go around. This applies to their latest recruit, Fuka Kazamatsuri, as well.
The main character in the game Divinity II: Ego Draconis is on their way to being initiated as a full dragon slayer when they get turned into a dragon. Your dialogue options allow them to protest this and act as if they are still a slayer until the slayer commander and their slayer buddies attack the main character.
Ashrah of the Mortal Kombat series is a demon who wields a holy sword that purifies her bit by bit with every one of her fellow demons that she kills. She hopes to become completely purified and holy this way.
Balthazar from Baldur's Gate II: Throne of Bhaal. He knows the Bhaalspawn aren't Always Chaotic Evil, but thinks they're still too dangerous, and he intends to kill himself last in a ritual designed to stop this from bringing Bhaal back. He actually works with some of the other powerful Bhaalspawn because they want to kill all the others except themselves.
Alex Mercer spends most of Prototype killing the viral monsters controlled by Elizabeth Greene, including Greene herself. Alex qualifies because he is the virus.
If he befriends or becomes the lover of The Warden in the original Dragon Age: Origins, Zevran Arainai becomes one of these in Dragon Age II. In the seven years between the end of the first game and the point at which Hawke meets him in the second, he has sown chaos in the ranks of his former employers, the Antivan Crows, managing to assassinate one of the seven Guildmasters while simultaneously forging an alliance with two more as well as several other disaffected assassins.
The Grey Wardens technically qualify, as becoming a Warden involves drinking Darkspawn blood and taking the Taint into themselves, turning them into a type of high-functioning ghoul with their humanity intact. This also allows Wardens to permanently kill the Archdemon by forcing its soul to Body Surf into them at the moment of death, destroying them both.
Played straight if a Mage Hawke ends up being Templar-Aligned at the end of the game. If still alive, Carver will call them out on this and points out that if Bethany was still alive, Hawke would be turning against her as well.
Bethany can be convinced to do this in the Templar Ending by a Warrior or Rogue Hawke, although she's not happy about it and only agrees because innocent people are being killed in the crossfire.
Demon hunters in Warcraft study and use fel magic in order to more effectively hunt demons. Since the magic is innately corrupting, many of them become partially demonic themselves and may or may not retain their original noble intentions.
Death Knights, former slaves of the Lich King, use their knowledge of necromancy and Scourge tactics to fight the undead in Northrend. A lot of the more vengeful Forsaken fall into this category as well.
Wrathion is a black dragon that, due to the unique circumstances of his birth, is free of the Old God corruption that has taken over the rest of the Black Dragonflight. He's on a crusade to eliminate the tainted black dragons, and the rogue legendary Fangs of the Father questline is centered around helping him do this. By the end of the quest, he claims to be the Last of His Kind, though observant players have noticed there is at least one other black dragon (Sabellian) unaccounted for.
The Dragonborn in The Elder Scrolls V: Skyrim is a mortal with an Aedric dragon soul who fights other Dragons. The trope is played even straighter in the Dragonborn DLC, when the Dragonborn is forced into a confrontation with Miraak, the First Dragonborn.
If you choose to side with the Dawnguard vampire hunters against Lord Harkon in the Dawnguard DLC, Harkon's daughter Serana will join you and eventually be permitted to take up residence in the Dawnguard's headquarters. She can be convinced to cure herself of vampirism... but only if you say the right things, and only after Dawnguard's main quest.
If the Dragonborn is a Vampire or Werewolf, this trope can occasionally come into play. Defied in Dawnguard, as Isran will frequently chastise and refuse to deal with a Vampire Dragonborn until they cure themselves.
In Dark Souls, the most common enemies the Chosen Undead will encounter are other Undead who have long since gone Hollow and insane.
Off-Road Velociraptor Safari. The driver is a velociraptor for no particular reason. Its motivation is not really explored, but the way it is beamed away when time runs out suggests it may just have nothing left to lose.
Raziel in Legacy of Kain is a three-fold example. A former Sarafan vampire-hunter, resurrected as a vampire, he was betrayed by Kain, the vampire who sired him, and executed, then reborn as an ethereal wraith and accepted an offer from the Elder God to become an Angel of Death. His purpose is to hunt down and destroy the vampires who were once his brothers, but he also hunts and kills other ethereal beings, as well as members of the Sarafan Order, at times.
Subverted in League of Legends. Miss Fortune is a pirate hunter because her mother was killed by pirates, but her attire is completely pirate-like. A Pirate Girl? Nope, she's just dressing up like one, she's a full time pirate hunter.
Played straight with Vi, however. She was once a normal criminal, but then found a set of Power Fist in a mine. Afterwards, she redirects her passion into hunting down other criminals by punching them in the face, before becoming an official police in Piltover.
In Immortal Souls, Raven had herself turned into a vampire specifically so she could take revenge on the vampires that killed her family and is well-known for her enthusiasm about the matter.
Raven: You wanted to see me, Isis?
Isis: Indeed, Raven. I have a new mission for you.
Raven: Do I get to kill vampires?
Isis: Still holding a grudge against your own kind?
In the backstory of Darksiders and its sequel, the Four Horsemen were the only Nephilim who believed the Nephilim's campaign of universal conquest was wrong. The offered their services to the Charred Council to help set things right. The newly christened Horsemens' first order was to slay the rest of the Nephilim.
The vampire twins Vania and Veight, as well as the player (who gets vampirized by them) in the "Memories of the Dark" event in the mobile trading card game Rage of Bahamut.
In Sword of the Stars, the Liir's greatest weapon against the dreaded Suul'ka power-mad Liir Elders who enslaved the rest of the Liir so they could live forever in space is The Black another Liir Elder who lives in space like the Suul'ka.
Othar Tryggvassen, Gentleman Adventurer!, from Girl Genius, is a Spark on a quest to kill Sparks (eventually even the good ones, but for now just the bad ones). He's even outright stated that after he rid Europe of all the other Sparks, he'll end his own life just to ensure that the Spark is no more.
A puzzler. All Sparks must die, yet I am a Spark. I will kill myself when my mission is complete, but now I can kill myself first. Tempting.
Also, in the card game, there is a "vampire hunter" character that ironically is the only card that counts as "vampire".
In Chirault, Kiran is a demon and employed by the demon hunter guild. That said, in Chirault, "demon" is a pretty broad term, and Kiran's "species" of demon (horned humanoids) seems pretty rare. Many of the demons that Kiran kills seem to be non-sapient.
In Were Geek, Joel attempted to turn one of the Hunters into a geek, with somewhat predictable results.
Starfire Agency had Timothy Madoc, a vampire hunter who was turned as a sort of sick joke. He and his living siblings made a pact that when they wiped out every other vampire on the planet they would slay him. Unfortunately he outlived the rest of them by several hundred years, and eventually he actually became an enforcer for the vampire council after they banned killing mortals. And he's the "uncle" of main character Alexandra Maddock.
Ryo from Heart Core, a demon hunter from New Ayers. The story heavily implies that she is a demon herself, being able to sence their precense from long distances and surviving falling off a skyscraper. Her reasons for killing demons are not yet fully known.
This trope is actually played with because everyone on Earth, except White Knight, is infected with nanites, the things that cause people to turn into EVOs. That means everyone at Providence is hunting down their own kind and anyone of them could randomly turn into one at anytime without warning.
In the Backstory of Adventures of the Galaxy Rangers, Shane Gooseman was the youngest and most advanced of the Artificial HumanSupertroopers. When the 'troopers rioted, Shane was the only one to remain loyal. However, the Earth Government only allowed him to live on the condition that he hunt down and kill his renegade ex-comrades — or bring them back to Earth to be sent to their deaths in cryo. Shane hates this hellish bargain, but can't see a way out.
Slimer from The Real Ghostbusters is a ghost that lives with the Ghostbusters and helps them against other ghosts from time to time (i.e., almost every other ghost in the Containment Unit was caught with Slimer's help).
In Scooby-Doo Meets the Boo Brothers, the Boo Brothers are ghosts that work as ghost exterminators. They claim that that's the whole point. ("It takes one to catch one in this business," they claim.)
The Legend of Korra brings us a rather prominent member of the anti bending supremacist faction, the Equalists, who is himself a waterbender. Specifically, it's the leader of the movement, Amon, who has dedicated his life to ridding the world of bending.