It's an anime but speaking of bad guys who think what they're doing is good/justified/right, I immediately thought of Light Yagami from Death Note. That one's interesting because it's all from his perspective, but he's the one doing the bad stuff.

I still have to think up redeeming qualities for my antagonist. {e:ponders}

"Whoever fights monsters should see to it that in the process he does not become a monster. And when you look long into the abyss, the abyss also looks into you."-Nietzsche