What really is a Villain?
I think in the End it's all about perspective of oneself and how others see you.
Sure. Sometimes it is the cowardly Criminal who sees an opportunity to finally wants to make a shortcut in live, pulls a Ski mask over it's head and decides to rob a Bank, or it's the poor street urchin who pickpockets people on the Subway just to survive.
It's always societal Norms that teach us what we are supposed to see as good and what to see as evil. Laws of Justice are made by Countries and Men and not by the universe.
Is a Person who chooses to stand up for it's own cause, for the Defense of it's own people who are maybe mistreated by said society, who despite this prides itself of being just and righteous, really the bad one?
How does one see her-, him or itself?
Maybe it's just your normal Day to Day job in an oppressive regime which the rest of the World happens too perceive as ''Evil''.
Maybe you were born with an mutation that gave you a bad reputation from the start. Having the ability to boggle the minds of other people can be a hard burden. Was it your fault to be born this way? Or is it their Fault to fear you. Maybe they should fear you. Maybe you should use your Powers to Help others who were cursed with a similar Fate.
Maybe a shadowy Organization working for your own Government. Kidnapped you, mutilated you and imprisoned you in this horrible robotic body and only by Luck you managed to Escape. What are you willing to do to survive? Don't you want to get revenge at these people who otherwise would get scot-free out of any lawsuit you could throw at them and wouldn't they doom others to similar fates?
Maybe you were the humble Apprentice for a powerful, but arrogant and lazy Wizard who let his awesome powers be controlled by petty rules and dusty old Books. Who forced you to menial shores despite your own great potential.
Maybe you are a brilliant Scientist whose accomplishment got you mocked by your peers. Women and Men of science. Intelligent People. WHO DARED TO LAUGH ABOUT YOU!
So what you can't raise the Dead via the use of a chemical Formula and make them do your bidding. You must show them. You must show them all!
Or Maybe. Just maybe. Only your brilliant and selfless leadership can safe this insane and rotten World from itself. Which is why you have to conquer it whole!
There are many more reason why People may become things Society sees as ''Villains''.