Those are some pretty good theories, people! Man, my memory’s going in my old age, how could I miss the Citan/Shion connection? (then again, I only played the game once, about six years ago.) Ah well, it’s a good reason to replay a great game, excellent even by today’s standards. Right now I’m replaying FF7, but I’ll get to XG eventually.
One theory: The entity inside DEUS said it was from a higher plane of existence; this must be the same one that Nephilim (and perhaps the Gnosis?) come from.