Possibly a spoiler, just to be careful:
Spoiler for A Theory for how C.C. survived:
I think it might not be so much that C.C. is "still" alive, as much as it is that she's "alive again."
What I mean is, could she have a Miang from Xenogears thing, where if her current body dies she just awakens in another female body or something? It seems a bit too big/grand-scale for this series, since that would mean origin-of-life and stuff is involved, but it would certainly explain how she's there. And she's certainly not a ghost.
