@GeekyPotato I know that feeling, but every time I've tried to just start over, I got too intimidated and went back to what I already made :D
Maybe you just need to look at it from a different angle.
This is purely my view on this, but if I were to write something using your plot, I'd start with Hanna mybe discovering her powers (or whatever seeing the world differently would be called), then being capture or something by this organization, who explain what Hanna is currectly experiencing.
Maybe they make her feel like this power is wrong, or a sickness, or something, so she will go along with the tests so she can get rid of it. There she meets the other characters you've mentioned, and they figure out that the organization is lying, and they try to stop them, for example.
Of course, you can do this in flashbacks, so teh reader only gets a few pieces of information at a time, and when they re-read it, it will all suddenly make sense, but I find this unnecessarily difficult (I'm also kind of lazy) :D