My Most Difficult Character

My most difficult character right now started as a supporting character, with a very small role to play, and turned himself into another main character. I wasn't expecting him, nor did I want him, but it turns out I needed him. And now that I need him I have to spend time figuring out what it is that he wants, which he isn't willing to give me freely. He ends up helping my protagonist in a way that makes the story more believable, she wouldn't be able to do some things without inside help from him, but I just can't figure out why he helps her. He is supposed to be one of the bad guys, one of the people she is trying to defeat, for lack of a better word. Does he suddenly have a conscience or change of heart, did something happen in his past that made him flash back and realize he was on the wrong side? All the other characters he is associated with believe so strongly they are doing something good that they are blind to how wrong it is. So why not him? That's what I'm trying to figure out and this particular character is making me work much harder than I anticipated. Perhaps it's because I doubted his need in the first place, who knows. Maybe that is what motivates him now; vindication.