"You either die a hero or live long enough to see yourself become a villain."—Harvey Dent, The Dark Knight
Alright, The Hero has saved the world, paid off his debts, and made time with that girl in the blue dress. His story is done, the credits have rolled, and there was no "To Be Continued", but what's this about a Sequel? What could the guy be in for now?
...Wait, who are these new people? And where's the character from the Original?
WHAT!? He's a villain now!? What happened? He went rogue.
Usually, the new main character is Locked Out of the Loop, and doesn't know something that the original character does, or the other way around (or perhaps both) and they're at odds over it. Of course there might be other reasons, but in these cases it usually ends with the new characters and the original cast working along the same side.
A subtrope of Sudden Sequel Heel Syndrome; also compare with Not as You Know Them. Also note how these heroes seem to avert the Bag of Spilling. See also Previous Player Character Cameo, when the old PC isn't a major antagonist.
- Yomi in Ga-Rei Zero. From helpful mentor and friend 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.
- Sasuke in Naruto Shippuden.
- Jacen Solo in Legacy of the Force.
- 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  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.
- Caim, the protagonist of Drakengard, appears about halfway through the sequel as the "One-Eyed Man" responsible for the death of Nowe's adoptive father. He's basically the same person he was in the first game. He's just not the viewpoint character any more.
- 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: Sons of Liberty. 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.
- Kain, the main character from Blood Omen: Legacy of Kain, was the Big Bad of the sequel Legacy of Kain: Soul Reaver.
- 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.
- Clyde from Vigilante 8 turns heel in the sequel.
- In Final Fantasy IV: The After Years, the kingdom of Baron is once again aggressively invading its fellow nations in order to take the Crystals. However, this time, the king of Baron is Cecil... a Brainwashed and Crazy Cecil.
- 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.
- Arguably parodied in I Wanna Be the Guy, where past versions of "the Guy" are player characters from many of the games homaged.
- Mega Man Zero sets this up with Mega Man X apparently leading the slaughter of an untold number of reploids. It's subverted, but you knew that.
- 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.
- Mario in Donkey Kong Jr.
- Most main characters in Nippon Ichi games, especially in Disgaea, are inevitably back as Bosses and antagonists in later games. Not because they've turned evil, mind you: They don't take kindly to other people stealing the Main Character spot.
- 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.
- Ethan Waber in Phantasy Star Universe: Ambition of the Illuminus. The events that cause him to go rogue are detailed in the online comic Shadow of the Arkguard.
- Lenneth Valkyrie from Valkyrie Profile is essentially the main antagonist (from Wylfred's eyes) in Valkyrie Profile: Covenant of the Plume, and can be the final boss (dependent on which ending is viewed.)
- In Prototype, Alex Mercer 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 Mechwarrior 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 Overlord Big 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 Ace Combat Zero the True Final Boss of the Brutal Bonus Level is Mobius 1, the protagonist and Player Character of Ace Combat 04 Shattered Skies. Later games with similar Boss Rush modes also add Scarface One of Ace Combat 2 and Blaze from Ace Combat 5 The Unsung War.
- 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.
- Jill Valentine in Resident Evil 5 as a result of being Brainwashed and Crazy by Wesker. She appears in Marvel vs. Capcom 3.
- In Tactics Ogre, there is a Gaiden Game for the Game Boy Advance called Knight of Lodis. Whatever happened to him? He becomes a Climax Boss in Tactics Ogre Let us Cling Together.
- 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-Hero Antagonist, as he has understandable non-evil (if selfish) goals which just end up opposing the other main characters' goals.
- actually preserving them in cards
- More specifically, the warrior class. The other two classes also turned rogue, including the rogue.