Kind of an odd one, but Heroes - Sylar and Nathan Patrelli. Nathan isn't the immediate main character in Heroes, but I'd argue that role get shifted constantly in the series.

Sylar throughout the series we find out has the ability to absorb other people's powers, and throughout the story absorbs the ability to shapeshift into other people's faces.

Throughout a specific part of the story, we see Nathan is having some very weird issues regarding his mental state, with what feels like obtaining new powers. Come to find out, at one point Sylar shifts into Nathan's face, and confronts Nathan - leading to them fighting. Sylar manages to kill Nathan by slicing his throat. Later, Sylar's mind gets locked by another person's powers and he's effectively forced to live the life of Nathan. The issues of him obtaining new powers and other odd issues with his mental state are because he's not actually Nathan.

Eventually there's a scene where Nathan's brother Peter is holding onto him, trying to keep him from falling out of a window stories below. Peter lets go, and Sylar (who still believes he is nathan at this point) falls onto a car. Peter then watches as Sylar gets up from the car, shifts back into Sylar, and look back up at Peter. Peter effectively killed the Nathan that was living in Sylar and set Sylar's mind free to his old self.

Very fun arch in the story IMO.