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In Claymore, the eponymous warriors are Half human half demons who choose to fight for humanity's sake. Just about every one who finds out that the organization which transformed them does not have the best interests of the citizenry at heart ends up going rogue.
In Silent Möbius, some Type 4 Lucifer Hawks ( Rally and Katsumi!) raised as humans decide to serve humanity.
The protagonist in Blue Gender has a "disease" called B Cells which are a form of Gaia's Vengeance. It's intended to cause humans to rebel against their peers and go kill crazy (which it does spectacularly to two other characters). He manages to stay sane despite the various hardships Gaia and humanity throw at him.
Ayato in RahXephon is part Mullian (basically a human subspecies with blue blood) and when his Mullian blood manifests, there's concern he'll pull a Face-Heel Turn and join the Mullians, but he remains a nice guy on the side of his friends.
Schwartz Bruder in Mobile Fighter G Gundam is this. He is a dead body occupied by the DG (Devil Gundam) Cells to live. Despite being made up by the cells of the Big Bad, he is the Devil Gundam host Kyoji Kasshu's physical manifestation, driven to save his brother and stop the Devil Gundam.
While most vampires revel in their non-humanity even if they fight for humans, Seras does everything in her power to remain as human as possible without neglecting her duties to the organization... which involve drinking blood in order to use her vampiric powers killing vampires that threaten humanity.
Alucard's a weird case. He'll gleefully slaughter people, but he also believes that monsters like himself are even less inherently noble beings. He truly believes that humans are the only ones who could ever truly defeat him, the way Abraham Van Helsing and his companions did in the past. Thus he has a loathing to humans who choose to become a monster to have a chance at defeating him.
In Nightwalker, Shido, a vampire, defends humans from the nightbreed. He apparently has been a vampire for a long time and at first he was not so friendly to humans, but later changed his mind.
In Trinity Blood, Abel Nightroad is a Cruznik, a being that feeds upon vampires (and is thus two steps above humans in the food chain). That doesn't stop him from devoting his life to defending humanity, and using his relatively harmless default form to masquerade as a normal human. He is an interesting example of a Pro-Human Transhuman in that he was a Designer Baby and thus born a transhuman. He was also originally quite anti-human.
Kira in Mobile Suit Gundam SEED is accidentally this, being a Coordinator fighting for an army consisting entirely of Naturals (in a war started to exterminate his kind!). Not really his intention: he only fights to protect his friends. When it's revealed that both sides have genocidal intentions, he and his girlfriend, Lacus, form the Three Ships' Alliance, which includes deserters from both the Natural and Coordinator armies, and want an end to the war. Naturally enough, several other Pro-Human Transhumans, including Lacus, Athrun, Dearka, and the Desert Tiger, end up in this faction.
This is invoked in Tiger & Bunny as all of the Heroes are trans-humans called NEXTs with extraordinary powers which they use to save people and stop crimes, all of which are recorded by Hero TV for people's entertainment.
Blade chooses to use his vampiric abilities as a Dhampyr and daywalker to hunt vampires.
In the original Thirty Days Of Night, sheriff Eben purposefully infects himself with vampirism and manages to save the survivors with his newfound strength. He then kills himself since he can feel the bloodlust coming on and knows he can't maintain his original self for much longer.
The second comic series, Dark Days, has an originally less-than-nice vamp pulling a gradual Heel-Face Turn (at first helping Stella out purely for revenge against the Big Bad, but later on out of genuine feelings for her); by the end of the story, he doesn't even try to feed on her, despite having the perfect opportunity, which is saying something as vampires in that 'verse are pretty much all bloodthirsty (in both senses) Always Chaotic Evil sociopaths from the moment they're turned, even if they were dedicated vampire killers just before. Unfortunately, after his resurrection, vampire!Eben is not quite so inclined...
The X-Men are a whole organization of mutants who behave this way.
Sasha Bordeaux, formerly a Batman companion and then part of Checkmate, was infected with the OMAC nanovirus to become a more advanced OMAC, with enough free will to coordinate and command the other units. That enables Sasha to rebel, destroy Brother Eye and later reclaim a less advanced, but more useful and human-like cyborg form for herself.
Michael Costner, a young thief and grifter is activated as a regular powered OMAC unit to help rebuilding a thrashed Brother Eye. A peculiar combination of guilt for his past as a common burglar, lack of self worth, his earlier bout with drug addiction and The Power of Love enable Michael to shake off his programming and fight against Brother Eye for the sake of the world and his girl. In the end, while his pregnant girlfriend Vienna acquires his very same powers and rushes to his help, she dies and with Brother Eye deactivated, Michael loses access to his powers. In a bittersweet ending, Clark Kent manages to have Michael and Vienna revered as heroes and saviors of the human race.
Dr. Manhattan in the beginning of Watchmen. Though this is actually his main character arc— he becomes less and less so as the story goes on, eventually getting to "Why would I save a world I no longer have any stake in?". By the end, Silk Spectre II must convince Dr. Manhattan that humans lives are worth protecting. It's the revelation that her father is The Comedian that does it - realizing the sheer improbability of human life is enough to restore his interest in protecting it.
Just about every superhero ever, or at least the ones that aren't space aliens or Badass Normals.
Gunn in Angel: After The Fall (a direct sequel to the Angel series). He is determined not to become a monster and continue being a hero, though he's really trying to prove he's better than Angel, who he blames for letting him get turned.
The Confessor in Astro City is a Batman-like hero who is secretly a vampire. He wears a cross as his Chest Insignia so the constant pain will help distract him from his thirst. After he's destroyed, his sidekick is surprised to find the Cross Breed, a local Christian super hero team, mourning him; they assert that as far as they're concerned, he was always doing the Lord's work.
Shinichi of Experiment is turned into a cyborg by Ai, but because he's the only one around, he has to do the masquerade and try to be as human as possible.
Defied in Ultraviolet, where a human tries to reason with the not-vampire heroine, saying she was human once, too. She dismisses it, saying that humans were who made her that way and then wanted her dead, so she owes them no loyalty.
In Thief of Time, the character Myria LeJean is an Auditor, an enemy of humanity, but upon taking human form she realises what it is she seeks to destroy and becomes opposed to her own people, in defence of humanity.
In Snuff, the Dwarvish demonic entity The Summoning Dark, vanquished by Sam Vimes, becomes his ally in the cause of law and order.
In Fred Saberhagen's Berserker stories, Hilary Gage, an artificial intelligence designed to mimic every aspect of the human thought process, continues to think of "himself" as human, at least with respect to interstellar politics, despite being very much aware of the fact that "he" has no biological body parts. Later, he downloads himself into a berserker warship's central AI, and has to make sure he maintains enough control to prevent the warship from continuing its fight against humanity.
In Old Man's War, the CDF consists almost entirely of elderly men and women downloaded into genetically enhanced pseudo-clones (the rest is even less human). During boot camp one guy asks why they're bothering to defend baseline humanity when their new bodies are the next step in human evolution. Sergeant Ruiz tells him he couldn't be more wrong, all the alien DNA in their genomes makes them sterile and thus an evolutionary "dead end". In fact one of the reasons for the advanced enlistment age is so most of the recruits would have grandkids back home they would want to protect from baby-eating aliens.
In Larry Niven's Known Space Pak Protectors evolved to be this, they are hardwired to protect their descendants no matter what, however they will attempt to exterminate any other sapients including other Paks (except for the rare few whose descendants are all dead and have dealt with it by protecting the whole species), and will even kill their descendants who have mutations. Humans evolved from a Lost Colony of Pak Breeders and have differentiated so far that Pak Protectors will destroy them if given the chance, however humans can become Protectors and are intelligent enough to rationalize that they should protect all of humanity. Unfortunately this includes using the virus that causes Protector transformation on an entire planet to kill off everyone too young or too old to become a Protector and create an army of childless Protectors to fight off the coming Pak invasion fleet.
In the Revelation Space universe the Conjoiners are a faction of Transhumans who use advanced nanotech to enhance their minds and physiology. When they learn of the Inhibitors coming to destroy humanity they make preparations to flee, leaving the "baseline" humans to their fate. However, their nominal leader, Clavain, defects in an attempt to warn human space of what's coming.
In Being Human the three main characters are a vampire, a werewolf, and a ghost who still care about humans and are trying to live as normally as they can.
This happens a couple of times in the new Doctor Who with Cybermen who haven't been 100% perfectly converted. Specifically, in "Doomsday" converted Torchwood head Yvonne Hartman shoots a bunch of Cybermen while repeating "I did my duty for queen and country...I did my duty for queen and country..."
In "The Pandorica Opens", Rory Williams' Unexplained Recovery as a Roman soldier despite being erased from history is discovered to be because he was really an Auton duplicate and Manchurian Agent implanted with Rory's memories. Despite being forced to shoot Amy when his programming briefly took over, his genuine love for her allowed him to break his programming and he vowed to spend the next 2000 years protecting the Pandorica with Amy inside until she could be safely revived. And he did.
Kamen Rider series does this as a tradition. For instance, the original show (also named Kamen Rider) involves the main character becoming a Shocker cyborg monster, but he didn't lose his humanity and used the same transformation to fight the Shocker creations. The shows that followed more or less follow the same idea of their ability to transform being related to the villain of the show.
In Kamen Rider 555, Orphenochs are supposedly the next evolution of mankind, and the evil organization forces them to attack normal humans (in hopes of siring more Orphenochs. However, about one in a hundred can be transformed; most just turn to dust.) Some just go nuts on their own. However, there's a trio of renegade Orphenochs living together Being Human-style. The Rider suits were created by the bad guys, but are not themselves part of the transformation, though for the main Rider, it turns out there's a very good reason he can use a Transformation Trinket that isn't supposed to work for humans.
Teen Wolf does this. Scott. He cares deeply for humans and innocents, even trying to protect the Argents when possible. In contrast Derek is fine offering the "gift" of Lycanthropy to those who crave it, outcasts, the ones who are emotionally damaged and with health problems. Scott is particularly upset at this because of the active hunting werewolves face, making that much more likely the new converts die... Assuming they don't kill someone first.
The Vampire Diaries has Stefan. Even though he is a vampire, he still tries to retain his humanity as much as possible.
Elena as a vampire. She still retains her compassion and empathy even after she turned.
MasterBook RPG The World of Species, based on the film Species. Humans are injected with some of Sil's DNA, causing them to gain some of her abilities. This allows them to hunt down and destroy Sil's progeny, but they have alien thoughts and personality traits generated by the DNA in their systems.
Dungeons & Dragons supplement Knight of the Living Dead. A lich brings a paladin of Torm back from death as an undead creature. The lich orders him to gather magic items to help the lich conquer the city of Waterdeep, but instead he decides to fight against the lich's forces and protect the inhabitants of the city.
In Warhammer 40,000, every Space Marine is a bioengineered Transhuman, yet they serve humanity with zealous ferocity. It helps that the transformation, and the very reason they exist, is explicitly to protect humanity better. Of course their methods of protecting humanity include ruthlessly exterminating anything that isn't human.
It does actually vary by Chapter to Chapter on whether they're the protectors of humanity or the executioners of the Emperor's enemies. Some of the nicer Chapters including the Ultramarines (who run a Lawful Good and comparatively pleasant sector of the Imperium), the Space Wolves (who pulled an epicWhat the Hell, Hero? on the Inquisition and actually had a small war with them at one point over it), the Raven Guard (who will save everyone or die trying due to their Tear Jerker past), and the Salamanders (who are the only chapter who actively protect civilians, making them something of an Ensemble Darkhorse in the fandom) count especially as this trope. The Flesh Tearers and Marines Malevolent, and especially the Chaos Space Marines, however...
Virtually everyone who's not a "flat" (unaugmented human) is some shade of this by default in Eclipse Phase. Not much of a choice since the vast majority of those who survived the hard-takeoff Singularity were transhumans (and the harsh realities of the setting will ensure that they stay the majority no matter what anyone has to say about it); in fact, the setting refers to transhumanity. Though there are exceptions such as the Exhumans (in particular the Predator sub-faction) and the Ultimates.
The Carthian Movement from Vampire: The Requiem aren't exactly advocates for humanity - some of their plans for alternative models of vampiric government rely on a steady supply of "cattle" - but of the various Covenants, they're the ones most likely to advocate for human ingenuity, believing that human models of civilization will point to a grand replacement for the standing model of praxis. One of their more radical factions, the Anti-Obstructionist Army, actually takes action against anyone who tries to Embrace a human, claiming that human thought is hampered by the somewhat cooling effect of becoming a vampire.
In Alpha Centauri, eventually you gain the technology to turn your people into transhuman "transcendii," who are basically energy beings via Brain Uploading. They're still loyal citizens, each and every one.
If one plays through Deus Ex: Human Revolution with a pacifist slant, this is how protagonist Adam Jensen identifies himself in any of the four endings.
In Mass Effect 3, if Commander Shepard chooses to control the Reapers in the ending, Reaper!Shepard - especially a Paragon one - vows to use them as a force for good.
Technically, Paragon Shepard became Transhuman during the second game, having been resurrected with cybernetic implants, as well as undergoing extensive genetic modification that not only gives them increased speed and stamina, but resistance to small arms fire and strong enough to wield weapons that when fired, would normally shatter every bone in a normal person's arm. Shepard is a Pro-Human Transhuman in either case; paragon Shepard is a hero who protects all sentient life in the galaxy, while renegade Shepard helps humans and nobody else.
In Dragon Age: Origins, part of the Joining Ritual to become a Grey Warden involves ritually drinking Darkspawn blood, where the Wardens willingly submit themselves to the Taint, becoming immune to it's effects (for thirty years), gaining the ability to sense the Darkspawn and rendering them the only ones capable of truly slaying an Archdemon, thus ending the latest Blight.
The Architect in Dragon Age: Origins – Awakening qualifies, although technically he's a Token Heroic Orc who is not so much concerned with preventing further Blights to help humanity as much as he desires to free the Darkspawn from the influence of the Old Gods. However, he's not been particularly successful so far, since the last time he tried to help he ended up accidentally causing the Fifth Blight.
On the other hand, the reason the Circles of Magi exist is because the Chantry, as well as a good chunk of the population, do not believe that mages can be reliably Pro Humans. This is mainly because of the TevinterImperium, which is ruled by powerful mages, and controlled much of Thedas centuries before. In fact, according to Chantry teachings, the Tevinter mages are responsible for creating the Darkspawn. There's also the little fact that every mage is a potential conduit for evil spirits of the Fade to enter the world.
A good example of a Pro-Human mage would be the father of Hawke who taught his mage children to use their powers responsibly and had his own Badass Creed where he reminded himself that his magic would "serve that which is best in (him), not that which is most base." Mage player characters can be this as well... or not.
The player characters Vent and Aile in Mega Man ZX are, like most people in this period, crosses of human- and Reploidkind, and fight to protect everyone. In the earlier series, Dr. Light is this, having become an infomorph and continues protecting humanity through aiding his "son" X.
All of demigods in Asura's Wrath are transhuman cyborgs, but Asura is the only one after 12,000 years that stands up against them for humans after they start slaughtering them to obtain their souls for more power.
In Warcraft III, Night Elf warlock Illidan Stormrage seeks demonic powers to prove himself to his skeptical brother and sister-in-law and ultimately fights against the genocidal undead Scourge. By the time of World of Warcrafthe's turned evil.
Taken even further in Crysis 3, where a protracted nanotech Fusion Dance has you playing as an amalgam one dead guy's body, another dead guy's personality, and both of their memories, with an artificially intelligent suit of Powered Armor holding it all together. You're about as transhuman as it gets, but still firmly on the side of humanity and more badass than ever.
In Infinity Blade the Deathless are revealed later in the series to be normal humans from a bygone era, who technologically altered their Q.I.P.'s and bodies to make them immortal, permanently at their physical peak, and grant them superhuman power. In the second game, it's revealed that Siris, the main character, is actually the Deathless Ausar the Vile, who lost his memories and lived on amongst normal humanity, but this fact doesn't stop him from fighting for humanity's freedom.
Keine Kamishirasawa of Touhou is a were-hakutaku who's described as the safest person for a human to be around.
Gilgamesh of Fate/stay night was created by the gods of his time to tie them to humans, ensuring the continued existence of the gods. Gilgamesh eventually came to love humans more than the gods and rejected his role in the gods' plan, choosing to rule over Uruk because it was worth ruling. Even Gilgamesh's attempts to unleash Angra Mainyu on humanity is driven by his belief that the best humans will survive and be worth ruling.
The Kingfisher: Vampirism doesn't make one inherently evil, but the pro-human vampires are few: mainly Helen, Vitus, Jack, Tristan, and Darren. Notably, some of the least powerful characters in the story.
Genocide Men believe that they are such, except maybe for Joey, using their ceramic skeletons, artificial glands, and suitcases full of ebola to hunt down and exterminate genetic deviants for the good of humanity. Though there are signs that their philosophy is flawed, and they turned most of the planet into deviants themselves in an attempt to make people immune to designer plagues and less violent, with a virus that killed over a billion people.
The Sephirotic Archailects and their ancestors, the early pro-human transapients, from Orion's Arm are this. The Archai are not specifically pro-human as such (humans are but a fraction of the 10th millennium terragen populace), but generally benevolent towards lower toposophic lifeforms and promoters of sophont rights regardless of singularity level. This is as opposed to the solipsist AIs, who just don't care about anyone else positively or negatively, or the ahuman AIs who will, at best, kick lower beings off of their turf, or, for the less fortunate, Mind Rape them to death or worse.
In Justice League, Gorilla Grodd intends to publicly kill the League because they are Transhumans fighting to protect humans, which, according to him, is contrary to natural selection.
The female lead hero Cyber Six from the animated show of the same name. While pretending to be a "normal" human by day and "becoming" the hero Cybersix and fighting monsters by night.