Example #1: Richter Belmont from Castlevania Symphony of the Night. At the beginning of SOTN Richter is shown defeating Dracula before a time skip. In that time Richter disappears from the world and we don't know where he went. 4 years later when Alucard shows up to Dracula's Castle in the true beginning after the prologue, after about half of the game we find Richter in Dracula's throne room trying to revive Dracula so he can keep fighting him. It is revealed that Richter is being mind controlled and after you destroy the thing controlling him, he joins your side.

  
Example #2: The Kamizono Sisters from Gal Guardians Servants of the Dark. When you play the first Gal Guardians game you play as a pair of Demon Hunters. In the second game you play as a pair of Demon Servants. All throughout the early game you hear other demons talking about these legendary demon hunters and when you meet them, they waste no time before trying to kill you. After you fight you realize it was all a misunderstanding and you work together whenever you see them again.

  
Example #3: Nagito Komaeda from Danganronpa 2 Goodbye Despair. While it doesn't technically apply here there is a bunch of evidence that implies that there was an intention to make Nagito Komaeda the same person as Makoto Naegi from the first game. Both characters share the "Ultimate Lucky Student" Talent which at this point was a first for the series. In both the English and Japanese dub, he shares a voice actor with Makoto Naegi. Several sprites are parallel between both characters. If you look at some of the early concept art for Nagito he looks even closer to Makoto with his outfit. If you rearrange the letters in Nagito Komaeda's name you can spell "Makoto Naegi" and have a leftover "Da" at the end. As for the way he behaves in the second killing game, he plays the role of an antagonist almost the polar opposite of Makoto causing trouble for you throughout the entire game. I went through the entire game thinking that he was secretly Makoto and that it would be revealed at the end.

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[Loved Trope] Playable characters that come back as antagonists/bosses in future entries.