How about an undercover Agent who was arrested along with everyone else he was tailing? He was sent to infiltrate a faction to lead them into a trap, steal intelligence, find their HQ, etc. but he was caught too early and his cover is so deep that he's sent to prison with everyone else. I'm thinking that the Agents betrayed him and left him in prison (they considered his powers too dangerous from the beginning and he was just a loose end), which makes for a good guy rapidly going bad.