I'm currently participating in NaNoWriMo, and the story I'm working on is a pretty classic-style sci-fi novel with a female protagonist. She's very sympathetic, a little goofy, and as it turns out several chapters in, she was/is MtF. It's thrown at her to ruin her credibility, and she has to confront her fears since she has been living in stealth for several years.
(Yeah, I know, but it's really better than it sounds, trust me!

*hugs*
*edited, changed to MtF due to brain issues at the original time of writing!