I'm not sure if I should explain, but here it goes.
It's a history about a transgender. I think it's a girl-born boy who hasn't made the transition yet at the beginning.
When we look at the mirror, we see a female reflection. After we give the mirror shard, she says "when you are ready come talk to me", and fades away.
Then we go flying around the vaccuum, the nothing, collecting pieces of ourselves to make the change available.
The girl in the tree might be a old girlfriend that don't accept our transexuality, we love her but she doesn't love the real us.
The girl in the moon is the image we idealize to turn. She was lost in the moon, the moon representing some kind of veil.
At the end the moon is destroyed, there is no hidding anymore. We go back to earth as a girl. The change is complete, she is finally free, that's why she closes her eyes, it's pleasure. It's not depressing, it's beautiful.
I love this game. Felt very lonely seeing all those people run away from me, while I was only trying to save them. The only companions but I wasn't able to get to them and befriend.. When the bridge was built, I just had to go back and see how they were, what else they accomplished, the grandsons of the people I saved. I felt a god, and it was horrible. Please make more games!