How about Shield agent Maria Hill is captured by Hydra and taken to one of there bases. There she is used in sexual "experiments" with mutants and in other vile ways.
That might have worked a few years ago but with the modern (well after Agents of SHIELD and Captain America 2 I think you'd be far better served either making up the groups and working from there with your premise intact or having them breaking Maria Hill to bring her over to their side. She's amongst the highest ranked SHIELD agents in the world and there is a lot of really grey area in the current Marvel Universe.
How about this, Maria Hill, with her new job at Stark Industries, is kidnapped while on a high security mission in her new capacity by Hydra, seeking access to Stark Tech. Or the story could be as you say, something like five years ago.
Either or works just fine. I mention it because based on what I've seen from the recent Marvel stuff I suspect we're going to learn something about how Hydra isn't really evil pretty soon.
Let's say this is some rogue or splinter Hydra group, even extreme for them. That they are targeting female members of intelligence and or security agencies all around the world. CIA, ex Shield, MI6, etc. So Maria Hill would be a "prize catch" for them.
Maybe they use sex to try and break them, for whatever reasons. Or, maybe they want to "breed" them with human/ mutants, or even human/alien hybrids to create some "superior" super beings.