It's really hard for me to write questions here without giving a complete info dump on my story. Every time I start to explain my problem, I find myself writing an entire synopsis. This is my third attempt.
Basically, I have someone who starts out as a protagonist. In the first part of the story, she saves the day by force of personality. The villain did something horrible at the end and completely deserves punishment, but he escapes at the last moment.
In the second part of the story, the villain comes to terms with his crimes and redeems himself. He changes his ways and starts a new life.
In the third part of the story, the original protagonist has spent her time obsessed with bringing him to justice. She fears people won't see how evil he is, so she decides that the ends justifies the means. She ends up doing some very questionable and possibly evil things to make sure he's caught, arrested and executed. She eventually ends up doing things worse than he ever did, but feels justified because she needed to do those things to get him caught. It works exactly as planned. And everyone around her sees her as a hero, but she knows that she's not. Her victory is hollow and she's not happy at all.
Anyway, I like the story myself. But I thought it might be off putting for readers to invest love for a character in the beginning who ends up going bad in the end. I am afraid people want clear lines between good and evil. Would they feel cheated if I slowly turned it all around?