So my story takes place in a super hero world but is about the vilains it's got a simple premise where nothing is black and white and the heroes are in some cases worse than the villains. My MC is a classic take over the world type he wants to rule humanity to remove war, disease and general conflict and his girlfriend/sidekick/partner is very loyal to him she wants what he wants and believes in him because she was the victim of human trafficking and in her mind what he does to bring about change is right because in the world he wants to make there is no real freedom or privacy but to her (keep in mind she's been severly traumatized by her own experiences) and it's worth whatever to create a world that is free of evil. Ironically she's more fanatical than he is. The idea is while they have a Harley/Mercy and Joker/Lex Luthor dynamic they genuinely care for each other to the point that he'd even consider giving it all up just for her because the world he wants to make would be worthless without her. Where as she'd consider that(sacrificing everything the both want for her) a betrayal because he promised to change the world when they first met. My only problem is I don't know how or if I should get her to strike out on her own. She acts independent but is actually very dependent on the MC and literally can't function on her own. She actually will have a panic attack if he gets captured because she wouldn't know what to do. She became a super villain after being bought and experimented on and forced to serve an even worse guy who the MC over threw and afterwards set her free she then heard his desire to remake the world and quickly wanted to be part of it. So she has not been on her own or made a decision for herself in a very long time. Any advice would be appreciated.
The problem with asking other writers for suggestions is you'll likely get what they would do. With that in mind, I'd first change the main character status to the sidekick, and make the story about her. She sounds way more interesting and has a greater range and room for development. She has a built in motivation-strength/fault/something to lose combination with her background and shared goal. Basically, go back to the learning the character inside and out phase and spend some more time on her. When you boil it down there are only two types of characters, those who change and evolve, and those who don't. In the long run I think the sidekick/girlfriend is going to offer the most to work with.
Do you love her? Maybe subconsciously you're being too protective. Do something mean. Write a few pages of how she gets her ass kicked by another villain. Then write another page of her getting even. That ought to give this girl some experience.
Hehe, that reminds me to Worm. (Which is a very good read.) Does she simply not have the talent to come up with plans or is it a psychological blockade? If it's the latter, I can imagine some kind of gradual process: Maybe (just suggestions - I have no clue whether any of that fits in with what you have already) she uses the main villain as a kind of projection area for her own urge of aggression, so that she doesn't have to act these out by herself and yet her wishes are fullfilled. I can imagine during her captivity she wanted to strike, wanted to free herself from her torturers, but had no chance. Aggressions were probably severly punished. She has internalized that, so she doesn't dare striking on her own, but when her partner does it, she is ok with it. She hides behind him. Uses him as a mask for her own wishes. Now, when he doesn't want to do it anymore, maybe she becomes the mask. Maybe she pretends to be him to the outside. (Manipulating images, sending letters claiming responsibility signed with his name... whatever) She could justify it by telling herself that he is only temporarily confused and she needs to fullfil his work before it's too late/before the chance is over. And later she slowly starts dropping the mask. Maybe she doesn't even notice at first, but her own will starts to show.