Yomi in Ga-Rei -Zero-. From helpful mentorandfriend of Kagura in the prequel anime to the Big Bad in the beginning of the manga. And then an even bigger bad near the end of the manga. She does lament her situation.
Bernkastel in Umineko no Naku Koro ni, if we're going by the reasoning that she is the summation of all the non-post-Matsuribayashi and Saikoroshi-hen incarnations of Rika Furude.
Kamen Rider Decade plays with this as Tsukasa/Decade spends Final Chapter hunting down all the Kamen Riders, while the Riders believe that they must stop Decade's rampage in order to save The Multiverse. In the end, Decade turned out to still be Good All Along, as his trying to "kill" the Riders *
actually preserving them in cards
was the only way to save the Multiverse and the Kamen Rider legacy.
This is how you appear to your former squadmates in Mass Effect 2, seeing as how you're currently working for Cerberus, a terrorist group whose members were shoot-on-sight enemies in the first game. Ashley and Kaidan outright refuse to go with you because of it, and Tali rejoins with serious reservations about the Normandy's Cerberus-comprised crew (they attacked her people, so It's Personal).
Lloyd Irving in Tales Of Symphonia Dawn Of The New World is seen as a murderer at first, in stark contrast to his ideals in the first game. Emil hates him for killing his parents in a brutal massacre of Palmacosta. Of course, he's not really a villain. The Lloyd who committed those crimes was Decus wearing a disguise.
Isaac in Golden Sun: The Lost Age is an unseen antagonist to the game's main character, Felix. Felix intentionally avoids contact with Isaac, because he knows they're working against one another, and wishes to avoid a fight — until Felix's supposed allies Karst and Agatio try to kill Isaac, at which point the groups are forced into an uneasy alliance. (And eventually team up for real once Felix convinces Isaac he's right.)
Felix was an opponent to Isaac's group in the first game, and The Stinger for the first game made it fairly clear you'd be playing as Felix in TLA. Neither Isaac's goal nor Felix's has changed, so they're still at odds. Effectively, it's the player who's gone rogue.
In Armored Core for Answer, AC4's main character is the pilot of White Glint, the NEXT leading Line Ark's military force. You can fight her in the storyline, or you could side with her. Either way, she loses the storyline fight.
Subverted in Metal Gear Solid 2. At the start of the Plant chapter, Raiden is repeatedly told that the leader of the terrorists is Solid Snake. Ten minutes of gameplay and one Paper-Thin Disguise later, you realize you were an idiot for thinking it was possible.
In Devil May Cry 4, Dante is an example, showing up as a villain right out of hell, and making himself a serious enemy to Nero, the new protagonist. They do end up fighting for a similar cause later, especially when it's revealed that the guy that Dante gunned down, and who got better, is the Big Bad.
You learn of a possessed and evil character in Diablo II, called the Dark Wanderer. As it turns out, he's the player character of the first game*
More specifically, the warrior class. The other two classes also turned rogue, including the rogue.
In Mysteries of the Sith, the player character for most of the game is Mara-Jade, and the previous player character Kyle falls to the dark side for the final boss fight.
Misleading trailers were released to make it seem like this would be Yuri in Shadow Hearts Covenant. The trailer made it seem like two new characters would be the leads and Yuri only appeared at the end after turning into a monster. When the game came out though, Yuri was the main character and almost all the scenes in the trailer never occurred.
Richter Belmont was the main character of Castlevania: Rondo of Blood. Five years later for Symphony of the Night, Dracula's castle is back, with Richter in charge. In truth, he was manipulated by the magic of the dark priest Shaft.
When the Zero series was in production, the real X was in fact supposed to be the big bad. However, executive meddling forced Keiji Infune to continue the X series beyond five which also forced him to alter the Zero series a bit.
In .hack//G.U., Kite's avatar from the first games is used as an evil AI. Also, Elk shows up as Endrance, who plays the part of a villain for a good portion of the game.
In Prototype, AlexMercer fought to stop the infected and Blackwatch from destroying New York. Prototype 2 has him spreading the infection, including to the new player character, James Heller. The reasons for his Face Heel Turn, given in a Motive Rant towards the end and a prequel comic seem to be out of line with his characterization at the end of the first game.
J.C. Denton, the protagonist of Deus Ex, becomes one of the major faction leaders in the sequel, Deus Ex Invisible War, and is also arguably the character who is most centrally driving the game's plot (a role that usually falls to the Big Bad). You can join his faction in one ending path (and the majority of the game's plot seems to be building up to this), but if you chose any of the other 3 ending paths he becomes the "final boss" of the game since assassinating him becomes one of the key endgame objectives. Denton has changed quite a bit between the two games, but can still arguable be described as a "good guy", and Invisible War is much more Gray and Gray Morality than the first game.
This seems to be the trend in the Necro Vision series. The protagonist of the prequel ends up becoming the Disc One Final Boss of the main game, while the protagonist of the main game either becomes the Devil's right-hand General or (in the hardest to obtain ending) ends up becoming the Lord of Hell himself. In either case it's pretty clear he'd be the Big Bad if any sequel was ever made. In both cases they turned to the dark side with the intention of preventing a greater evil from occurring.
The sympathetic and seemingly good-natured protagonist of Mech Warrior 4 is revealed to have turned into a cruel despot in the expansion pack, and serves as a Disc One Final Boss. In his case it may have been In the Blood, as he obtained the throne by overthrowing his evil dictator uncle.
In Arcania: Gothic 4, the Evil OverlordBig Bad is King Rhobar III, aka the Nameless Hero, the protagonist of the previous 3 games. it turns out he's possessed by a demon lord, though, and gets exorcised in the ending.
This happens quite a lot in the Contra series. The most notable are Contra: Shattered Soldier and its sequel Neo Contra. In Shattered Soldier it's revealed that the terrorist leader and Disc One Final Boss is in fact Lance Bean, Player 2 of the classic Contra series, who as it turns out is a Well-Intentioned Extremist trying to stop the World Government from destroying the planet, but who was driven insane by the Red Falcon cell he injected into himself to survive an early assassination attempt by the World Government. In Neo Contra, Bill Rizer (Player 1 of the classic series and Shattered Soldier) is the Big Bad and final boss, who wants to destroy the Earth For the Evulz ( although it's heavily implied that he's actually an insane A.I. based off of Bill's mind, with the real Bill Rizer being The Obi-Wan character). Lucia (Player 2 of Shattered Soldier) is also a member of the Quirky Miniboss Squad and seems gleefully evil in helping Bill destroy the world. Unlike Bill, she dies without any explanation being given for her abrupt Face Heel Turn.
Also happens retroactively in Hard Corps: Uprising, where the main character is a young Colonel Bahamut, who was the Big Bad of the original Contra: Hard Corps.
Tekken series would have this. Kazuya is the protagonist in the first game, but becomes antagonist in the second game up to the rest of the series. Jin is the protagonist in the third game onwards, and becomes the antagonist in the sixth game.
In Dead Rising 2: Off the Record, Chuck Greene appears as a Psychopath, having failed to save Katey in this continuity. Similarly, Stacey is the Big Bad of the game, replacing Sullivan.
Agent Washington in Red vs. Blue, who makes the switch between seasons 6 and 8. Though arguably he ends up not a villain but as an Anti-HeroAntagonist, as he has understandable non-evil (if selfish) goals which just end up opposing the other main characters' goals.
