JoJo's Bizarre Adventure has Dio Brando. One of his closest followers proclaims that he "loves him as he loves God" while the other one cuts off his own head when Dio merely asks him for a bit of his blood. The rest of his legions of followers that he doesn't outright brainwash are all insanely devoted to him and all too eager to announce that devotion. Hol Horse is the only exception, being an amoral cowardly mercenary who only serves Dio out of fear and constantly looks for ways to backstab him.
Ribbons Almark from Gundam 00. Which is only appropriate, since he's a stand-in of Scirocco.
Flit Asuno becomes this in the second generation of Gundam AGE after witnessing Yurin's death at the hands of Desil Galette, which leads him to becoming the savior for the corrupt and genocidal Earth Federal Forces.
Griffith from Berserk is a definite example. He cares for the weak and helpless everywhere, fights tyranny and cruelty, and everyone loves him. However, after getting imprisoned and tortured to within an inch of his life, he sold his soul to the evil Godhand to become its fifth member Femto, hired demons as enforcers, and ruthlessly killed anyone who opposed his rise to power, including the Band of the Hawks that he once led, whom he sacrificed in order to become Femto in the first place.
And in a later arc, Griffith is called an actual Messiah by the people. He has the Crystal Dragon Jesus equivalent of the Pope proclaiming him to be the best thing since sliced bread. We, the readers, can only cringe in expectation of the devastation that will ensue. And to make it even worse, since he still possesses at least a significant amount of a Godhand's power even though he was supposedly reborn as a human, and seems to still be backed by the other four demon lords, he actually IS a Crystal Dragon Antichrist, who is currently posing as a Dark Messiah. No matter how bleak things are already, they WILL get much, MUCH worse.
Bishop Mozgus from the same story in Berserk may be a lesser example — a dedicated destroyer of evil forces who took in and nurtured deformed, sick, and dying orphans, giving them hope in a world without any...aaaand then trained them to be his torturing, murdering inquisitorial hitmen.
Meanwhile, the stories actual messiah (or the one who comes closest to it), Guts, is seen by the people as The Antichrist and has only a tiny band of followers who at least try to understand how the world really works.
Lelouch Lamperouge, the main character of Code Geass, who seeks to overthrow of The Empire that killed his mother, Lelouch means well (most of the time), but even at his best, he's shot a dog or two — some of whom he even unleashed himself.
Aion in Chrono Crusade seems to fancy himself as one of these—at least, for his fellow Sinners. He preaches that his dream is "freedom" and it's his goal to achieve it, at any cost. He's willing to (and does) sacrifice his followers and himself if it means his dreams will be realized.
Arguably, he became a straight Messiah later on, since his dying act was to restore Konoha, and other characters even commented on him sharing the destiny of "bringing a great change to the world of Ninja" with Naruto.
Tobi tried to pass himself off as this at first. Naruto called him on it being a load of crap, and he agreed.
But with the reveal of Tobi's true identity, it seems that he was being sincere about his claims after all, having pretty much been appointed to this role by Madara Uchiha himself.
Madara himself. He grew up in a warring states period that claimed most of his family, and learning that chakra was originally a gift that the [[Precursors Sage of Six Paths]] intended to connect humanity, but instead ended up escalating wars, so he determined that the only to peace was by becoming the Jinchuriki to the Juubi and trap the entire planet in a Lotus-Eater Machine. And along the way he does a ton of terrible things, betraying his former best friend Hashirama (and blaming the world for the suffering he endured after that despite being the one to instigate the fight and all the slack Hashirama cut him the past), using the Tailed Beasts for his plan and seeing them as little more than tools, and insists on being the one to bring about his new world and planned to sacrifice Tobi to do it, and stated outright he was even planning to betray Tobi to become the Jubi's Jinchuriki if Naruto and Sasuke hadn't defeated him first.
In the Grey and Grey Morality world of Ghost in the Shell: Stand Alone Complex, it's really hard to designate any characters as really good or evil. However, Kuze is the country's most dangerous top terrorist, who is fighting for the cause of the Korean and Chinese refugees that have to live in massive internment camps in Japan as third class citizens. In one of his first appearances, he tries to cut off the Prime Minister's head with a katana while she is meditating at a temple, and his ultimate plan is to build nuclear bombs and hide them in major cities, forcing the government into cooperating with his plans. To his men, he's not only a great leader, but becomes something like a religious figure. Which really isn't helped much by his white hair and skin and preference for white longcoats. While some of his methods are radical, he turns out to be one of the nicest guys around by the end of the season.
Dartz from Yu-Gi-Oh! was trying to destroy the world and rebuild it without the flaws.
Son Gohan during the Cell Saga turns into this when he turns Super Saiyan 2, as the transformation starting to cause him to take the bloodthirsty and sadistic Saiyan traits, but even though the heroes get creeped out by it, he's fighting an Omnicidal Maniac that makes it clear if he's not stopped will hunt down and kill everything on Earth.
Makishima Shougo from Psycho-Pass committed a number of terrible murders in order to provide awareness for people to live like human beings.
The Claw from GUN×SWORD, where people he has meet practically worship him like a god and are willing to do anything he asks or to make him happy. This including killing anyone that gets in the way of his dream.
Shishio Makoto from Rurouni Kenshin, whose goal is to eliminate the Meiji government, which he views as weak and inferior (and even his enemies don't deny that point), and start a new era in Japan in which everyone must live under his rule, and only the strongest can survive.
Most of Saint Seiya'sBig Bads have been some flavor of this. The Pope / Gemini Saga wanted to protect the world and thought Athena was too weak to do it. Poseidon thought humans were destroying the planet and wanted to flood the world to start it over right. Hades is the odd one out, he just wants to kill everyone so he can rule over the dead world. His minions however believed him to want to create a land without suffering.
Hades/Alone from Saint Seiya: The Lost Canvas is especially poignant because his reasoning to kill everyone is that, since life is pain, by becoming an Omnicidal Maniac and god of the land of the dead he can ensure they spend eternity in a painless Heaven analogue. However then the real Hades retakes control and wants to proceed with plain old mass genocide, no utopia.
Mars in Saint Seiya Omega wants to save the world... specifically, by saving Mars (the planet). However that requires draining the Earth of energy and using it to make his planet a paradise. He'd move the humans who swear allegiance to him to Mars.
Messiah from Undertaker Riddle wants to open the door that will join the living world with the afterlife and change their places, meaning all the dead souls of the afterlife will be resurrected but all the livings will die.
Adrian Veidt (Ozymandias) in Watchmencauses the deaths of millions in order to unify the world and prevent the nuclear Armageddon he believes is otherwise inevitable. The comic itself refuses to either obviously support or condemn his actions.
Abu Adallah in Shooting War masterminds a conspiracy against the US military occupation of Iraq, and dies for his cause. He engineered a nuclear apocalypse in the Middle East and Southeast Asia.
Ra's Al-Ghul is partially immortal, and his intelligence and Magnificent Bastardry can only be matched by Batman. With an army of devout followers to boot. In one alternate history, he completely conquered the world, and killed off all the super powered heroes.
The Batman Annual story Messiah of the Crimson Sun features a genocidal villain who intends to Death Ray the world and remake it in his image. It's Ra's.
Glorious Godfrey of the New Gods, who preaches the word of his master, Darkseid, all in the name of taking over the universe.
Avengers' foe Korvac during The Korvac Saga. Despite his claims of wanting to bring order and prosperity to the universe, his eagerness to kill and control others reveals him to be an evil savior-want-to-be.
Magneto. He'll do anything to make the world a better place for mutants, even if it means terrorism or all-out war. He has often been nicknamed by his followers as the "Mutant Messiah", and stands in darker contrast to his friend and counterpart, Charles Xavier.
Magneto himself has recently referred to Cyclops as this, as his many morally gray actions have restored the mutant race that once seemed doomed to dwindle into extinction.
Cain in RoboCop 2 is the leader of a drug cult who treats him as a messiah-type figure who will bring the world peace and prosperity through his designer narcotic, "Nuke", despite his tendency to be rather nasty to his critics and betrayers.
In the James Bond film Moonraker, this was suggested with Hugo Drax, given the loyaty of his followers.
Star Wars: Anakin Skywalker. It's played with somewhat as he makes a deal with the 'Devil', Palpatine, essentially acting as an Anti Christ. But in the end, he saves the day, fulfilling the Messianic Archetype role.
The main villain in Waterworld leads a group of pirates onto "Dry Land" in a prophet-like manner, and it involved raiding a settlement and killing everyone in it. It is even lampshaded, given that he was referred to as "The Deacon", which means a minister of sort.
Bane in The Dark Knight Risesis unambiguously this, and a Magnificent BastardÜbermensch to boot. However, it turns out that while he is willing to die for the cause, he doesn't actually care about 'liberating' Gotham at all, and whether he even believes that destroying Gotham will help make the world a better place is ambiguous. He's just devoted to the Hidden Villain, whose plan this was.
Loki in The Avengers. In Thor he's more of Anti-Villain, trying to raise Asgard's prominence by destroying their enemies in Jotunheim but by The Avengers his plan has changed to this.
In The Chronicles of Riddick, the Lord Marshall is worshipped by the Necromongers with almost religious reverance. He is the half-dead post-human who has pilgrimaged to the Underverse and returned a holy Galactic Conqueror. His rule is absolute and he is destined to lead his people beyond the 'Threshold' to the alternate realm, although he's not immortal; the post is permanent until the Lord Marshal either dies of old age or is killed by an aspiring commander, and a new Lord Marshal succeeds him.
Subverted in Lord Of Illusions. Nix presents himself as a dark savior to his cultists and they remain slavishly devoted to his revelations even after his death. When he returns he sacrifices them without a second thought for being unworthy of him and denies being their "shepherd".
In life, Nahalla in The Ghost Dance was a leader of a violent cult offshoot of Ghost Dance religion, which strove to hurt the white overtakers as much as possible.
Mina, introduced during the Age of Mortals for Dragonlance is one of these. First, during the War of Souls trilogy, she's (unwittingly) the messiah-like figure for Takhisis, the God of Evil (well, Goddess of Evil) for the Dragonlance setting. In the Dark Disciple trilogy, she then becomes this for Chemosh. Culminates in her ascending to the position of a lesser goddess in her own right, the Goddess of Tears, embodiment of sorrow and pain.
Paul Muad'Dib from Dune; curious in that he recognizes the dangers in his Messiah-ship, and sought to avoid them, but had the Dark Messiah moniker forced on him by his followers and reluctantly adhered to the mold.
His son, God Emperor Leto, saw it as well, but realised that he couldn't avoid it. He knew (hooray for prescience!) how future generations would see him, and was prepared to pay the moral price. Justified, in that failure to follow through would have meant the extinction of humankind. Maybe, following a path generally blinds one to other alternative paths
Lord Asriel in His Dark Materials. Though his plans include, in the short term, separating an innocent child from his soul to rip the universe apart (environment be damned) and he is portrayed to have a very haphazard respect for human life, ultimately, he's trying to allow everyone to live in freedom of thought and government, by destroying the angel who claims himself as God. Even the heroes don't like him that much.
Nyarlatothep in H.P. Lovecraft's work often appears as a messianic figure, gathering large amounts of followers by various demonstrations of power, and seemingly working for the good of mankind. In reality, his goal is no less than The End of the World as We Know It. May be more of an Anti-Christ without the connection to Christianity, though.
By the third book in KJ Taylor's The Dark Griffin trilogy when he embraces his destiny, Arenadd most definitely fits this trope. He doesn't care how the Southerners leave his country, but they will go; letting him kill them is just a bonus.
"Yet one shall be born to face the Shadow, born once more as he was born before, and shall be born again, time without end. The Dragon shall be Reborn, and there will be wailing and gnashing of teeth at his rebirth. In sackcloth and ashes shall he clothe the people, and he shall break the world again by his coming, tearing apart all ties that bind. Like the unfettered dawn shall he bind us, and burn us, yet shall the Dragon Reborn confront the Shadow at the Last Battle, and his blood shall give us the Light. Let tears flow, O ye people of the world. Weep for your salvation." Dark enough for you? Initially, the Dark Messiah in question, Rand Al'Thor, struggles heavily with the unthinkable notion of women being harmed. But as the books progress, he becomes increasingly disturbed, and the prophecies' promise of a world-shattering salvation seem to become increasingly more likely. Regardless of what actually happens, the Prophecies have certainly promised a Dark Messiah rather than a Messiah.
Many of the Dragons seem to be this. Lews Therin Telamon was seen as this because the Dark One made Lews Therin go crazy after saving the world by sealing the Dark One away, but the ensuing insanity amongst the male half of the magical population lead to the Breaking of the World.
Masema would be a good example, except that he's the (self-proclaimed) "Prophet of the Lord Dragon", not the Dragon himself. He and his ragtag army of Ax Crazies go around randomly slaughtering whole villages for not serving Rand devoutly enough. Rand keeps telling him to stop, but...
In the last book Demandred sets himself up as one of these as Bao the Wyld, a propecied figure for the Sharans also called the Dragonslayer. It's unclear if he really is Bao the Wyld or simply hijacked the prophecy, but the former is indicated to be more likely.
Jagang of the latter Sword of Truth books can inflict mental torture on those who can use magic and whisper into the minds of those who cant. He's also a rapist and generally terrible human being and the leader of a horde of fellow ones. He even has his own false prophet guy who sets up the religion of evil and has a scheme so they can practically live forever, luckily they both get killed their followers send to another dimension.
Kellhus from Second Apocalypse eventually becomes much like this. He might well just be a Villain with Good Publicity posing as a Dark Messiah, though. (Fans debate this.) His POV sections later on are careful to dance around his real motivations.
Ras the Destroyer in Invisible Man is almost a deconstruction of this type—he thinks he's going to be the leader of a revolution against white power, but in truth, he's a ridiculous figure who's easily manipulated by the Powers That Be.
Agent Ben-Canaan in Exodus is a little like this. Though he is not vicious as such, he is cunning, and can be ruthless when put to it.
On the other hand, he really isn't "dark" enough to quite fit this.
Kelsier from Mistborn: The Final Empire is like this right down to dying for the cause in the well-substantiated hope that his death will enrage the masses enough to make them rise against their oppressors.
The Lord Ruler from the same series is a Dark Messiah made good. Turns out, he actually did save the world from an Omnicidal Maniac about a thousand years ago, but turned it into a hellish totalitarian theocracy in the process.
Immanuel Jeremiah Branch of Mike Resnick's The Branch is a strange variation of this. He is the Messiah promised in the Old Testament but is completely self-serving and evil.
Harry Potter: Lord Voldemort is certainly seen this way by his Death Eaters in the few glimpses we get of their interaction. Provides an interesting contrast with Harry's more traditional Messianic Archetype. Voldemort even dies and rises again like Jesus and his satanic resurrection ritual is a perversion of the Eucharist involving blood, bones, and flesh.
The Dresden Files gives us Cowl, who, while presented as fairly antagonistic, repeatedly claims to be working for the greater good. Having a secret society that seems to include members of every single organization in the supernatural world, including a few renegades from the Denarians and an Outsider, doesn't improve his image. On the other hand, the man got a car flipped over on him and he tossed it aside, and allowed the guy who flipped it over on him to live, so...
Senna from Everworld could probably qualify for this trope—not only does she have a serious case of A God Am I (or rather, "the gods are idiots so I'm taking over"), but she manipulates a group of gun nuts from the Old World to form a cult around her to accomplish her ends.
Sauron from The Lord of the Rings, before he became the Evil Overlord he is more known as. He started out as an angel-like spirit, and turned to evil because he wanted to create harmony and control in Arda. Once he started listening to Morgoth, this turned into the desire to control all forms of life and rule the planet.
Zandramas and Harakan both try to set themselves up as these in The Malloreon.
Live Action TV
Adam Monroe of Heroes. Thirty years before the events of the series, he gathered twelve unique individuals to follow him, termed them his 'disciples', and attempted to save the world. Does this story sound just a little bit familiar?
One of those disciples, Daniel Linderman, also qualifies. A self-proclaimed "humanitarian", his stated goal in life is to "heal the world"...which he plans to start by blowing up most of New York. He also comes with a set of Healing Hands that can make the blind see and the lame walk, just in case you missed it otherwise.
And Volume Five introduced Samuel Sullivan, the leader of a very Cult-like carnival who is The Antichrist: he claims to be gathering together the "specials" of the world in order to lead them to a "promised land" where they can be free of Fantastic Racism, but in reality, he wants them because he becomes more and more powerful when he surrounds himself with more "specials", and he's hoping to boost his powers to god-like levels. (Which, incidentally, could easily lead to a Class 6 or possibly even Class X Apocalypse How.)
Jordan Collier in The 4400. He insists that everyone takes Promicin to gain powers, knowing that it has a 50% death rate. When a method is discovered to see whether you'd live or die if injected, he sabotages the attempt because it would "polarize the world between haves and have nots". Despite being at times manipulative and bastardy, he really was chosen by the people in the future to be the messiah, with the alternative implied to be even worse than a 50% death rate.
Gul Dukat was this for a bit in Star Trek: Deep Space Nine, when he lead a cult to the Pah Wraiths. Kai Winn exemplified this trope.
Stargate SG-1 has the Ori and their Priors, who use belief from billions of worshipers on thousands of planets to fuel their powers. The best example, though, is Adria: The Ori's Obstructive Code of Conduct (or rather, the equally powerful Ancients' Obstructive Code of Conduct, which they also enforce on their Ori cousins) prevents them from directly attacking the masses (except in their own galaxy, where anything goes), so their knowledge and a considerable amount of power was placed in Vala's asexually-conceived daughter, who rapidly grew into a beautiful, charismatic, and very deadly adult to lead the attack. She eventually had to Ascend to a Higher Plane of Existence to survive poisoning...and, as such, now falls under the Obstructive Code of Conduct that bound her bosses. Oops. Worked out well enough for Adria, though, since her bosses died in the interim, meaning that Ascension gave her all of their previously shared godlike powers.
A more mundane example pops up early in the first season, where the leader of another SG team ends up being revered as a god by the locals and goes on a power trip. He was implied to already be a little mentally unstable before, and the adulation and plight of the local population, coupled with spending a little too much time in the high-UV radiation of the planet's star, pushed him over the edge into thinking he was a god and trying to lead his people to self-destructive salvation.
Adam from Buffy the Vampire Slayer was specifically described as the Dark Messiah at one point, intended to bring about a new world order ruled by demon/human hybrids, and was good at inspiring demons to work for him (even Spike said so). The Master also intended to bring about his utopia by opening the Hellmouth, and was certainly treated with reverence by his subordinates.
Much as it has its own good Messiah in Locke, LOST has Ben, almost perfectly a mirror image of Locke in every way (and understandably pissed that Jacob apparently chose Locke to replace him).
Jasmine from Angel attempts to bring peace to the world...by employing global-scale mind control to disguise her appearance and make demands regarding worshiping her, eating scores of people along the way. The existing world conditions and the effectiveness of the actual heroes fit the bill perfectly.
Carnivàle has no less than two such characters: Brother Justin (aka The Usher of Destruction) and Sofie, the Omega, as revealed in the series finale.
Even the series' designated "good" messiahs (Ben Hawkins and Lucius "Management" Belyakov) can qualify as this. The series makes it clear that being designated as an Avatar of Light doesn't make a person heroic, and that the Avatars who are destined to do great things for humankind often wind up performing some truly horrific acts along the way. To whit, Ben wound up on a chain gang for murdering two innocent people before the events of the series, and Belyakov tried to assassinate Henry Scudder during World War I, and he manipulates several characters into killing each other over the course of the series.
The Following, Serial Killer Joe Carroll. He sets up a cult of like minded people, who practice "Carrollism", and murder people to the style of the works of Edgar Allen Poe. His followers even compare him to Jesus Christ more than once.
Ultimately, it's a Deconstruction of this idea, as the glaring problem with it becomes more and more apparent. He's a total sociopath who doesn't care about any of them, and they're all a bunch of total psychos. Things fall apart rather quickly.
In The BreakerNew Waves, Chun Woo seems to have embraced this role after he spent the previous series avoiding it. His sheer charisma and prowess is such that the people who survive encounters with him are eager to follow him afterwards.
The woman described in Edge of Sanity's "Crimson".
Hammerfall's song, "Restless Soul", seems like a great description of this kind of person.
Subverted by the Emperor from Warhammer 40,000. His Dark Messiah status was only established after his death and without his consent. During his life, he spent a significant amount of time fighting the people trying to establish a church around him. Part of the reason of the crapsack state of the world at the moment is because of the Horus Heresy, which put The Emperor into a coma so he could no longer prevent the church being established. Ironically, it was caused by Chaos showing Horus a vision of the future where the Emperor was a Dark Messiah.
Thanks to a Retcon, the Tau Ethereals went from visionaries uniting their people with great oratory skills and charisma to a caste of Dark Messiahs, being seen as leaders of the Tau's belief system while supposedly secretly controlling the entire race through Mind Control pheromones. Essentially, they can be seen as equivalent to Covenant Prophets in Halo. How did they not piss off the folks that liked the Tau being the only source of pure goodness in the universe? By stating all this through fluff; namely, the somewhat self-serving logs of Imperial xenobiologists.
Though Word of God states that this wasn't a retcon, it was always the case. They just didn't make it obvious enough.
Also helps that all that still makes them some of the most noblest leaders in the setting.
Lorgar, the Word Bearers primarch, thought of himself as the traditional Apostle, with the Emperor as the Messiah, but when he fell (after the Emperor told him off one too many times for worshiping and making others worship him), he wrote the book on chaos worship and, ironically, the book on Emperor worship before the Emperor tried smacking some sense into him. The Lectatio Divinatus laid the entire framework, even down to the way of referring to the Emperor in the Divine tense, years before the Horus Heresy and Lorgar's fall into the worship of Chaos.
In Warhammer, the Everchosen are the chosen champions of the four Chaos Gods who are determined to conquer the Old World for Chaos. The current Everchosen is Archaon. To everybody else the Everchosen is the Anti Christ.
Vlad von Carstein tried to conquer the Empire to put an end to the infighting and save from Chaos. Like many other characters in the setting, how begin his intent was is debatable.
In Exalted, everyone can be this. Canonically, the Scarlet Empress and Chejop Kejak are among the purest examples of this trope: both have killed millions and sacrificed small children because they believed that it was the only way to keep Creation from annihilation. It's an open question whether there was a better way.
Also, Abyssal Exalted, fitting in with the whole dark-mirror-of-the-Solars theme. Their signature martial art? Dark Messiah Style.
And then we have the Malefactor Caste of the Infernals, corrupted Zeniths who serve Cecelyne, the Endless Desert, whose entire gimmick is creating societies based around strict, repressive laws. Her Charm suites allow her servants to create holy lands (by inflicting desolation because deserts are her thing), reap Essence from worshippers more effectively, interact with and feign being an entity of the spirit world, and answer the wishes of their worshipers. The best/worst part? It's implied that her core philosophy— that all laws are ultimately made to assist the strong in dominating the weak— may, in fact, be right. That's not very reassuring.
Nicolas Kerensky, of BattleTech fame, eventually came to believe that violence was an immutable trait in humanity that could not be eliminated, but could be harnessed. To this end, he created The Clans; a society based off Might Makes Right, Honor Before Reason, and eugenics in order to isolate the damage caused by warfare to those who actually fought it. To achieve this, he took absolute power, and when one of the Clans had issues with his ways of running things, he wiped them out and eliminated all records of their existence.
Asmodeus, the ruler of Hell and greatest of the Archdevils, plays this role in Golarion, the setting of Pathfinder. To wit, his church and personal involvement staved off destruction through civil war in the powerful nation of Cheliax. As a result, his church is the official religion, his priests and inquisitors hunt down heresy and proscribed faiths, and his faith and the government are intertwined. The society runs on predation, with the government openly allowing, regulating, and even owning the trade in slaves, gladiatorial combat, the flesh trade, and so on. Devils secretly move through the society, pulling whatever string their lords demand. But Asmodeus' involvement did stop the country from falling apart, and Cheliax remains a Wicked Cultured powerhouse rather than an anarchic nation torn asunder. Even better, Cheliax views Hell as its servant, not the other way around.
The Hell Knights view Hell's order as a thing to emulate as they try to undo the chaos of Golarion, and look to Asmodeus' vision of rulership for guidance. Surprisingly, they are Lawful Neutral, not Lawful Evil, despite their terrifying appearance and open admiration for Hell.
Kane of the Command & Conquer: Tiberian Series is the military and religious leader of the terrorist group-turned-superpower Brotherhood of Nod. A seemingly immortal genius tactician, brilliant inventor (who patented the first Tiberium-harvesting technologies) and charismatic speaker, who is also ruthless. His followers certainly regard him as a Messiah who will herald the next phase of mankind's evolution. Also fulfilling the Messianic Archetype, he is betrayed by countless Nod Generals who feel he went too far. By Command & Conquer 4: Tiberian Twilight, he approaches GDI with a proposition for an alliance in order to save humanity from extinction via Tiberium. Everyone expected him to betray them rather quickly. In the end, he didn't. Turns out, he's actually an ancient, immortal alien imprisoned on Earth since times immemorial. The Tiberium Wars and the business with the Scrin was in aid of his ultimate goal: escaping via Ascension.
Dr. Wallace Breen from the Half-Life games. He legitimately believes what he is doing is the only way humanity can survive, from surrendering humanity to the Combine all the way to helping the Combine oppress humanity. The worst part? He may be right.
To a certain extent, Count Bleck in Super Paper Mario seems to be one of these, as his plan involves destroying all the current worlds so he can create a better world to replace them afterwards. In reality, he's an Omnicidal Maniac and plans to destroy all worlds and then kill himself, leaving nothing behind.
World of Warcraft's Sylvanas Windrunner seems to generally want to help her people and, presumably, the other races too. She seems much more (positively) emotional (though still very cold) than most other undead and is portrayed about as sympathetically as possible for a character bent on the utter destruction of all her enemies so she can raise them into undeath with her. Oh, and while she seems to have a bit of a setback due to Varimathras, most of her really nasty plagues and poisons are still around whenever she feels like killing everyone.
The new Silverpine Forest questline shows her to explicitly support the raising of new Forsaken using Val'kyr. This saves the future of the Forsaken race, since they have no other means of reproduction.
Kain R. Heinlein of Fatal Fury strives to build the ruins of Southtown into an independent utopia. His preferred means of doing so is by culling the weak from the strong through combat, and mercilessly killing the weaklings and parasites in his city.
Gill, the Big Bad of Street Fighter III. Such is his influence and charisma that he was actually able to rebuild the Illuminati. His brother, Urien, is very unhappy with that, and wants to take leadership of the cult himself.
Similarly, The Master from the first Fallout seems to come off as this to many a Super Mutant.
Archer (and the rest of the guardian spirits) from Fate/stay night. Making a long story short, they work as the Earth's Immune System: stored in a timeless pocket dimension, the Earth summons them to prevent incidents that would threaten humanity or itself (like, say, drilling for mana). They do this by hunting down and killing/destroying everyone related to the incident, innocence be damned, and then return to their pocket dimension. Archer is practically the patron saint of this because he recognizes it as the most efficient means of saving people, even if he hates it.
Emir Parkreiner, aka Garcian Smith, in killer7. The reasons why are... obscure.
The two gods, Kun-Lan and Harman, their agents on earth, Emir Parkreiner and Harman Smith, are all dark messiahs. The gods don't generally care what their agents do as long as they achieve their ends, resorting to murder and enslavement. The real problem is that they work for the East and the West, respectively, and are constantly at war with each other. So whoever wins, someone else loses. This is shown in the ending of the game, which lets you decide, ultimately, if the West will be destroyed, or the East.
The "noble" Prophets from Halo are the leaders of a religion who's goal is to kill all sentient life, sending us all to the after-world.
On the other side of the war is Master Chief himself, being called Demon by the Covenent, even after the seperatists ally with the UNSC. He's destroyed the titular Halo (twice) and Space Noah's Ark (they even call it that).
Meanwhile, the Gravemind seeks to bring together the galaxy in unity and peace...by killing and infecting everyone with the Flood.
Both Kain and Raziel of the Legacy of Kain series fit to some degree. At first, Raziel is called "pawn and messiah". Then Kain is accused of having "messianic delusions". Then both are represented as messiahs of two competing races. Then it turns out Raziel is both messiahs and Kain is actually a completely different, higher kind of messiah. I've gone cross-eyed.
Harbinger: Human, you've changed nothing. Your species has the attention of those infinitely your greater. That which you know as Reapers are your salvation through destruction.
A Renegade Shepard can fit this trope as well, due to the ruthless nature which he/she exhibits. Subverted with Saren, who at first seems to be one of these, but it turns out that he was being controlled by Sovereign.
Both Daisy Fitzroy and Father Comstock from BioShock Infinite. Ironically, they both have a personality cult while being ideological opposites. Comstock also intends to raise Elizabeth as this, breaking her will through a combination of torturous experimentation and time so that she becomes his heir and reenacts his version of the Final Judgment upon the "Sodom below".
In Deus Ex: Invisible War, Saman, the supposed leader of the German branch of the Order, is revealed to be the leader of the Templars, a terrorist group that seeks to neutralize all biomodification technology, thus eliminating the power that maintains the rival Illuminati.
Anders in Dragon Age II. He spends much of the game pointing out the injustices the mages suffer at the hands of the templars, such as the beatings and rapes as well as the Rite of Tranquility. He's the leader of what he calls the Mage Underground and compares himself to Andraste, the world's Christ and Joan of Arc figure. And at the end of the game, he blows up a church full of people to start a war between the mages and the templars, fully expecting to be martyred for his actions. Whether Hawke sees him as a messianic figure or not is up to the player to decide, but Anders certainly fancies himself one. Averted in the Rivalry path — Anders will admit that there was nothing messianic at all about his act of mass murder. Rather than a messiah, Anders will see himself as just another monstrous Abomination that needs to be put down.
Hawke. Even if you play as Messianic Archetype, Hawke's choices ultimately serve as the catalyst for the Mage-Templar War, as the Champion of Kirkwall becomes a rallying cry for those wanting to be free of Templar oppression. As Varric's framing story can attest, a lot of good people have died in Hawke's name, while far less know who Hawke actually was as a person.
Septerra Core presents Doskias as this. He truly believes that he is the Saviour of Septerra. Too bad he seems to be more the Destroyer of Septerra.
In Dark Souls, the Chosen Undead becomes this if he/she refuses to relight the First Flame and becomes the Dark Lord.
By Resident Evil 5, Albert Wesker essentially became this: Gathered several followers and organized what can only be compared to a cult? Check. Has superhuman powers? Check, although he technically had those since post-Resident Evil. Believes himself to be God at the very least? Check. Seems to think his actions in spreading Uroboros across the planet Earth in a jet bomber is "saving" the planet? Big fat check!
In Dark Savior, the parallel realities storyline comes to a head when protagonist Garian must prevent his own Evil Counterpart from becoming this and bringing ruin to the world.
Micaiah in Fire Emblem: Radiant Dawn slides into this territory later in the game.
In the roguelike Dungeon Crawl Stone Soup, if you play a Hill Orc character you can choose to worship Beogh, god of the orcs, whose priests fit this trope to a T. Your character is considered a savior by orcs you come across, some of whom will even join you in your quest. Among your other powers you can even walk on water. All of this has led to the Hill Orc Priest's popular fan nickname "Orc Jesus". That said, the Hill Orc Priest is not a benevolent figure, or at least not to non-orcs; Beogh's stated goal is the extermination and/or enslavement of all non-orcs (as well as "heretic orcs" who refuse to serve him), and he's implied to have ripped out an angel's tongue for not accepting him as the one true god.
Big Boss/Naked Snake in the Metal Gear franchise. After being betrayed by his country a lot and finding out that the only place he feels truly alive is where he fights, he manages to gather similar-minded soldiers, all of them with combination of force and charisma that they all loyally follow his footsteps to make his dreams of a world where soldiers are always needed come true. Even he makes male followers attracted to him too.
Lord Xykon and even Redcloak's brother Right-Eye believe Redcloak is full of it and that his Dark Messiah act is nothing but an excuse for his inexcusable deeds. The real reason Redcloak is so committed to the Plan is because quitting now would mean that the deaths of all the goblins that occurred in the name of the Plan (many of whom were killed by Xykon for fun) including Right-Eye whom Redcloak murdered to protect Xykon would have been for nothing. He can't face shouldering the blame for all those deaths.
Redcloak's God, The Dark One, was this before he Ascended to godhood.
Baron Wulfenbach, from Girl Genius. Formerly, the Anti-HeroLancer to a pair of traditional messianic types; he was a minor noble who was exiled after an attack by The Other. When he returned, he found chaos reigning in Europe. So he conquered everything and became a ruthless dictator to maintain order and peace. And it worked. Showcased here.
Last Res0rt has Veled, the 'Messiah of the Endless', who has gone on to become Ziligo's head of the military, although she comes off as more Necessarily Evil because of her precarious political situation.
Homestuck: After Gamzee goes sober, he starts believing that he is both of the Mirthful Messiahs worshipped by his Juggalo religion. Which is somewhat true, considering that he's a descendant of the Grand Highblood. As such, it is now his glorious duty to subjugglate all the lowbloods and paint murals with their blood.
As it turns out, he isn't the Mirthful Messiahs, and never believed he was. Said Messiahs do exist however, and he eventually started serving them.
Amon from The Legend of Korra fits this trope. He leads the Equalists, an Antimagical Faction that wishes to rid the world of bending, claiming that benders oppress the non-benders of the world (and he's not entirely wrong). His status as a Dark Messiah stems from how he claims to have been chosen by the spirits to replace the Avatar as the world's savior, believing that the Avatar has failed to balance the world as promised.
Villain Has a Point, heck, several points when the rest of the story starts playing out with the next season — even if what he does with them is highly dodgy. Let alone how he goes about doing what he wants to achieve. It's what makes him a scarily effective version of the trope.