Few points worth addressing on your story:
-Whether the rest of your story is original or not, amnesia has been done, done, and then done again. It's really just getting old, and in your specific storyline I don't see him having amnesia as a major part of the game. There's more creative ways to get the same effect, I'm thinking.
-Why would Millie take him back to her people, when she is (I assume) aware that they are very racist against people like him? Seems like a very, very, very poor decision on her behalf, and one most people wouldn't make.
-The council seems like it's making a bad decision, as really - why make such a compromise with this boy they have such loathing for? I mean really, they seem like extremists to me - who really don't mind killing their own people for breaking laws, or outsiders. If anything, I'd see them coming to the decision of just killing the two of them, so either it was poor characterization on your part of these people, or there needs to be another motive not to just kill them both.
My opinions

Sorry If I restated anything that's already been said.