* The Master: In Doctor Who the Master is one of the Doctor's greatest enemies, but during the Time War he decided to run and hide by making himself human. In this form he gained a human identity as Professor Yana who was a good man desperate to save what was left of humanity from the death of the universe, though sadly this identity was erased when the Master was returned to normal.
* Third Overlord: A twist in the first game is that the Overlord you play was the eighth hero who tried to kill the previous overlord, who had secretly taken over the Wizard's body. The game lets you choose between pragmatically "saving" the lands in order to rule it or just killing everyone, but even if you pick the former it's a big change considering that when a hero he fought against a corrupt ruler to free the lands. 
* The Iron Giant: While it's not explained why, the Giant was designed to take over/destroy worlds but lost all memory of this when arriving on Earth. Thanks to Hogarth the Giant learned to care about others and understand why killing was wrong, and decides that he doesn't want to be a weapon and instead chooses to be like Superman by saving the town.
* Stickleback: A ruthless gang leader and self-proclaimed "Pope of Crime", Stickleback is introduced as a selfish character who cares for only a select few and has a mysterious past, and it becomes apparent that his name, accent and even his hunchback are a disguise. It turns out that he's actually Sherlock Holmes, who suffered injuries after surviving the Reichenbach Falls and lost sense of his identity, and developed one based on vague memories of his enemies such as Moriarty.

A hero/villain lost their memory and ended up developing the opposite morality.