My MC he exists in a world of super heroes and villains and he falls into a gray area. He considers himself a good guy but a lot of what he does is morally questionable. The worst thing he does involves his love interest and she's a super villain. He is in "love" with her and he's basically her stalker. He kidnaps her and goes 50 Shades and it's all to help "rehabilitate" her. Her backstory is a tragic one and he knows it he knows she's in many regards a victim of circumstance and she's got an out of control animal side due to her powers and what he's doing is basically taming that side of her because she's incapable of controlling it herself and she gave up trying to. It's a lot more complicated than it innitially seems. However my MC he gets weird at times because it's got a lot of BDSM subtext. Now the reason he kidnapped her instead of approaching her is she's emotionally and mentally unstable because of her condition and he even states "I apologize for my rude manners but given how your condition affects your emotional state I knew you'd likely kill me before I even got a word out." and the thing this is true she's very temperamental and dangerous and at the same time it's not her fault because she was forcibly experimented on and the experiments left her leaning more towards beast than human. He's also doing it because people on both sides hero and villain want to put her down because they believe she's too dangerous and he believes because she's very feral taming her like an animal is the best solution. However it's very grey because she's still capable of rational thinking and logically she sees him as crazy but her animal side grows fond of him and she is very much distrustful of him it's complicated on her end it's easier to say she has mixed feelings towards him. Best way to describe it she hates that she behaves like his pet and that she can't control her behavior because she's not fully human anymore. However enough of her is still human to fully despise her situation. I'm just wondering though how far do I take this? I mean what lines shouldn't be crossed?
You can cross as many lines and take this as far as you want. Just as long as you recognize that this isn't a "good guy" in a "grey area." A sympathetic bad guy is still the bad guy.
Write it how it feels you should to start with. once you've finished the story, re-read and see how far it needs to go and rein it back in then. Like Cave Troll said, have fun with it. That's what first drafts are for. let the story and the characters run wild. Editing is there to help with anything morally questionable. You may find that your MC starts reading differently after you've finished.
I agree with what Thaddeus said, let the first draft just go buck wild and see where it lands. This is where you're not only discovering a lot about the character, world, setting, and so on, you're also getting the ideas down in print. Editing is for going back and saying 'yeah that stays', 'get rid of that', 'tone that down a bit', and so on.
Research Stockholm syndrome.... Also have you ever seen homeland? Where the MC in the first series was captured by a terrorist organisation and without spoiling the plot they convince him to join their cause and betray his country through breaking his will to a point. It is quite convincingly done. Might be worth a gander, sounds quite similar in a sub plot way.
