The villain is evil; he does evil things to the world's people. The hero (a.k.a "the good guy who does good things and is against the villain") wants to stop this evil, and goes in a journey to face the villain and stop him. However, in order to achieve that, the hero ends up also doing things considered evil.
Now, maybe this could be used in the plot, something like "You came to stop my evil, but look at you, you've become just like me".
But I'm not sure. Wouldn't it be contradictory?
Edit: Oh, please, I know this is cliché, I'm just asking about the good-guy-becoming-evil stuff, everything else is just an example.