Shinji Ikari from Rebuild of Evangelion fits this much better, as unlike Gendo he was genuinely saving the world until Gendo tricked him into dooming humanity.
Yu-Gi-Oh! GX: Judai's Heroic BSoD causes him to transform into the villainous Supreme King once he decides to use evil's methods to fight evil itself, complete with a literal gaggle of Fallen Heroes (evil versions of his normal Elemental Heroes).
In Yu-Gi-Oh! 5D's, Rex Godwin qualifies. Before he became the tyrannical head of Security, he was the legendary Mysterious D-Wheeler who tried to build the Daedalus Bridge and connect Satellite to Neo Domino, hoping to free the residents of Satellite from the oppression of the upper class. But Security had other ideas. When they tried to arrest him, he drove his D-Wheel off the incomplete bridge, vanishing, becoming a martyr to everyone who followed him. In a sense, when he became a Dark Signer, he was a Well-Intentioned Extremist, who sought to put a stop to the conflict between good and evil that seemed doomed to repeat itself endlessly. When he was finally defeated, the Daedalus Bridge was completed as a modern bridge, and stands as a symbol of the man he once was.
Prétear. Along with the revelation that the Princess of Disaster is the current form of the last Prétear, Takako, the show also plays with the possibility that anyone who becomes the Pretear could become the Princess of Disaster. Which naturally leads Himeno Awayuki, the current Prétear, straight into a Heroic BSoD while she sorts it out.
Gentle Chapman was one of the most admired Fighters ever, but after old age and an illness caught up with him, he could only win via cheating (perpetrated without his knowledge by his wife). He paid for it by dying...and was revived as a zombie by the Devil Gundam.
Master Asia also falls under this. He was formally a part of the Shuffle Alliance, a group that was devoted protecting humanity from self destruction, and Domon Kashu's mentor. But during the previous Gundam Fight, he saw how badly the Fight damaged the Earth and blamed humanity for despoiling their homeworld so carelessly. After meeting the Devil Gundam, he joined its plan to wipe out humanity, believing that it was the best path for life on Earth to survive.
Also Devil Gundam. It was built as nanomachine colony to restore Earth's environment, but Ulube wanted to use it as a weapon. When it escaped to Earth, the impact messed with its A.I and turned it into an Eldritch Abomination.
Ulube himself seems to fit in as well. He seems to have been genuinely heroic, if proud, until he lost to Master Asia, let his bruised pride get to him, and then began to plot to get more and more power...
Mobile Suit Gundam 00's Big Bad, Ribbons Almark, seems like this, considering that he was a Gundam Meister who piloted the very first Gundam in the series and saved Setsuna's life. It's actually a subversion, as he was never a hero. The intervention when he saved Setsuna had no glorious goal beyond a field test of the 0 Gundam, and he was supposed to kill all witnesses. He only spared young Soran Ibrahim because he saw the devotion in the young soldier. And this incident triggered his god complex, leading him to become the Big Bad.
Gale Raregroove, Pumpkin Doryu, and Captain Hardner in Rave Master.
Nagato, aka Pain was born with a special power that marked him as a literal messiah. Inspired by the words of his childhood friends and mentor, he desired to bring about a lasting peace. However, his pacifistic attempts left his friend Yahiko dead and him crippled, shattering his dream. So, he set out to create a new peace, by sharing the pain that he had suffered.
Hanzo, his predecessor as the leader of the Hidden Rain Village, also started off with good intentions before he became a Crazy Survivalist.
Belive it or not, even Orochimaru qualifies. Although he'd die before admitting it, there was a time, before his defection, when he legitimately cared about his teammates and fought on behalf of his village. After seeing many people die in war, he became obsessed with gaining immortality and lost any sense of ethics.
The Nine Tailed Fox could be argued to be this. One of the legends mentioned about him by Jiraiya and a toad made him out to be some kind of supernatural natural disaster that emerged to punish mankind when they got too evil and sinful. As he's very much sapient, regardless of whether or not he's inside a host, and if there is any truth to the legend, that means he chose to seek out and destroy evil wherever it emerged. Considering that the Tailed Beasts were all thought of as nothing more than convenient power sources to be exploited, that means that he could have eventually gotten tired of that nonsense and played the part of the asshole embodiment of evil that he portrayed himself as to be left alone.
Oskar Von Reuenthal in Legend of Galactic Heroes. Particularly tragic, since he did not rebel against Reinhard Von Lohengramm out of genuine malice or ambition, but because he was framed and was too proud to accept punishment for a crime he did not commit. His death is arguably the most senseless and undeserved in the entire series.
Ubel Blatt has a number of these, similar to the Overlord example further down the page. 14 heroes go to fight the Dark Lord. On the way there, 3 die heroically, and upon the entrance of the Evil Lair, 7 of the survivors get cold feet and stay behind. The other 4 go to defeat the villain, winning with great difficulty. Returning home, those heroes get ambushed by their former comrades and are bloodily murdered. They go on to become the "Seven Heroes, who defeated the Dark Lord and the '4 Lances of Betrayal'". The 7 Lances end up going insane with power, but can get away with anything because of their hero status. Though one of the 4 is back and wants revenge.
The Big Bad of Drifters is heavily implied to be this. Well, he's actually implied to be Jesus Christ turned Omnicidal Maniac. Plus, some of the Offscouring can qualify — Joan of Arc becoming a homicidal pyromaniac after being burned at the stake, for example.
Aga Mbadi from Battle Angel Alita: Last Order. He was once a renowned hero around the solar system for hunting down a dangerous terrorist. After being forced to watch the only woman he ever loved slowly die in his arms and acquiring his insane nemesis's brain chip, he has turned into a Manipulative Bastard who considers everyone but himself lower than dirt.
Jellal, before his brainwashing, was a legitimately heroic young boy, being the leader of the child slaves inside the Tower of Heaven and willingly risking his life to save Erza from torture and accepting it in turn. After Ultear corrupted him, he became the very antithesis of his original self, manipulative and self-serving so that he could revive the supposedly-dead Zeref. Even worse, Zeref wasn't even dead, so his plan wouldn't have succeeded even if he did win. After he finally breaks his brainwashing, he's horrified to realize what he's done and most of the world sees him as a horrible terrorist.
After having his alignment changed by the effects of Nirvana, it emerged that Hot-Eye of the Oracion-Seis was one of these. He originally just wanted to raise enough money to fund a search for his lost brother, Wally, but seemed to have gotten corrupted by his teammates somewhere along the line, though they themselves (sans Brain) were just as innocent, being fellow slaves of the Tower of Heaven alongside him. After all is said and done, he calmly accepts incarceration for his deeds while he was a villain, after finding out that the Fairy Tail guild members had met Wally not too long ago, and declares himself happy with the knowledge that he's alive and well.
Caster is Gilles de Rais, a knight who fought along side Jeanne d'Arc, before descending into madness after her death and turning into a Serial Killer.
Jinno from Afro Samurai. He was Afro's best friend as they trained together for years, but one night under the Bodhi Tree, he witnessed all of his friends and fellow pupils killed by bandits, and then Afro coldly murdered their master to obtain the No. 2 headband. He blames Afro for everything that happened, and had his ruined body fitted with cybernetics to turn him into a formidable warrior. Before Afro can challenge Justice, he has to fight past his childhood friend.
Lady Flair in the Dirty Pair Flash universe, a Former WWWA agent and predecessor to the Current Lovely Angels who after a mission goes bad and felt betrayed went on to become an assassin , but makes an heroic sacrifice after realizing the truth of what happened.
Suzaku from Code Geass was the poster boy for what an Eleven can become in Britannian society. When Princess Euphie dies, he turns into the White Grim Reaper. That said, he was already an Anti-Villain in deep denial over what he was really doing working for The Empire, but that is the point he started to cross multiple moral lines in pursuit of his goals.
In Fushigi Yuugi: Byakko Ibun, a prequel to Fushigi Yuugi, the audience sees a kind and silent man named Nirusha, who helps a much abused little girl to start looking for her place in the world. Towards the end of the chapter, it's revealed that said man is none than the horrifyingly cruel Miboshi from the original series.
Tokyo Ghoul :Re gives two examples, both corrupted by Aogiri Tree over the course of the two-year Time Skip between series. Hinami has gone from The Cutie that did her best to assist the heroes and wanted to live in peace with humans, to a Broken Bird that is a prominent member of Aogiri. She handles their intelligence network, and seems to have lost all compassion for humans. More extreme is the other example, former Plucky Comic Relief Seidou Takizawa. The idealistic Ghoul Investigator was Reforged into a Minion, and has become a deranged Half-Human Hybrid that appears to have lost his humanity as a result of extensive torture. He gleefully explains that I Am a Monster, and goes on a killing spree on the orders of the Big Bad.
Scar was once a warrior-priest who dedicated himself to his god Ishvala. However, the Ishvalan Rebellion took his family and the most of his people away from him, leading to him turning his back on his people, his culture and religion's principals and values in favor of his quest for vengeance.
Apparently Lieutenant General Raven used to be a kind and very good leader who placed the needs of his men first. Now he's a Insane Admiral who wants immortality.
Mikado Ryugamine in Durarara!!. The entire show appears to surround their own moral decline. Mikado started out as an ordinary, bored middle-schooler who wanted a more exciting life so he started the 'Dollars', an online gang based in Ikebukuro. However, as the gang became more and more real, likewise it became more criminal. Mikado then peacefully corrected this behaviour by suggesting that they should be a nice gang. He was absolutely ecstatic during the first Dollars meeting, where he got everyone together and stopped Namie Yagiri. Unfortunately, well before then, he had gained Izaya's interest. The informant began purposely messing with Mikado both overtly and covertly, he told Mikado he would always get bored of his life and would have to constantly change in order to keep it interesting and revealed Mikado's status as leader of the Dollars to Masaomi. He set the Yellow Scarves against the Dollars to cause a gang war and even involved the Slasher. Among the numerous other things, Izaya also arranged for the kidnapping of Non, Chikage's girlfriend, via the Dollars forum to start a large brawl, causing Mikado to want to remove the 'bad apples' from the Dollars. However, by this time, Mikado began to crack under the pressure and became a far more twisted person. He illegally obtained info on Dollars members he considered bad and had Aoba and his friends violently remove them. It becomes very obvious he's gone over the deep end when he calmly dismissed Celty's warning to not resort to violence and when he finally saw Masaomi again, told him he's 'not ready'. In the conclusion, Mikado threatened various gang members' families in order to enact his plan to annihilate the Dollars. He shot at Masaomi with a gun when the latter attempted to stop him. Despite missing, he revealed he had a second, concealed gun that fired on contact and shot Masaomi in the leg. Finally, in utter despair over what he had become, Mikado shot himself in the head. However, thanks to Celty, Mikado did not die and later ceased his gang-related activities to have a normal life.
Undefeated Bahamut Chronicle: Fugil Arcadia and Arshalia Rei Arcadia teamed up to stop the oppressive Holy Arcadia Empire and the rebels who resorted to increasingly radical and vengeful tactics. Despite their efforts, they could never get the two sides to make peace, causing them to become desperate and resort to more villainous methods. Arshalia created a massive Divine Drag-Ride, Ouroboros, to hypnotize the populace into forgetting their hatred. She also created Sacred Eclipse to both save people and kill those who are a source of conflict. When Sacred Eclipse pointed to her and Fugil as a source of conflict due to the entire world fearing them, she sets Sacred Eclipse to murder indiscriminately so that Fugil can defeat it and be seen as a hero. After she's killed by the rebel faction, Fugil spends millennia using Ouroboros and Sacred Eclipse in a misguided attempt to prove Arshalia's methods correct.