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Code Geassbut I'm sure there's tons more.
It doesn't necessarily have to be a plot twist, it can happen at the beginning and carry on from there. But it is cool to see the downfall/process of the hero slowly turning.
Basically the whole "you either die a hero or live long enough to see yourself become the villain" trope!
Banner by me (Dia)
Cocoa (c) MMPPP: Encore!