If you're interested in a story where the main character is one of The Bad Guys (tm), I'd like to recommend Worm, a web serial by John "Wildbow" McCrae.
I don't really want to spoil anything, so I'm just going to post the first part of the synopsis from Wikipedia:
Taylor Hebert is a parahuman who has developed the power to sense and control insects following a traumatic event. She lives in the fictional city of Brockton Bay, a hotspot of parahuman activity, and seeks to become a superhero. On her first night out in costume, she defeats a gang leader and is mistaken for a villain by a team of teenage parahuman thieves known as the Undersiders. Taylor infiltrates the team, hoping to learn the identity of their boss before turning them into the authorities. However, Taylor grows increasingly close to the villains and finds herself unable to betray them.
It's a huge work of fiction, and has some of my favorite characters of all time. I wouldn't say it's the most enlightened thing I've ever read, but it does deal with some powerful themes very well. I read it when I was 18, so I don't know if everyone will be sold on teenagers making up most of the main cast...But knowing what I know now (and having done a reread last year), I wouldn't let that deter you from giving it a shot.
If I had to identify a theme running through all of Worm, it’s Taylor wanting to make the world a better place, a safer place, for herself, her family and her friends. If I had to pick a second theme, it would be that those good intentions aren’t enough.