According to Wikipedia:
After God loses faith in humanity, the archangel Michael (Paul Bettany) is the only one standing between mankind and the apocalypse. He leads a group of strangers who must protect a woman who is pregnant with Christ in his second coming.
My first movie, an impossible-to-understand picture called (of all things) Apostasy, was based on Milton's Paradise Lost. Basically it took the position that everything in Paradise Lost was factual and that sometime in the near future some of the angels became frustrated with God not responding to Lucifer's return to Earth. From a theological standpoint it was somewhat complicated -- mostly because if you didn't know Milton you weren't going to have the foggiest idea what was going on with the atheist priest (played by moi) and his nun girlfriend.
So anyway -- with Legion they seem to be saying explicitly that God is on the wrong side. We'll see if that plays in the 3rd act.
If they'd made the third of His Dark Materials then we'd have seen (oh look, spoiler for a non-existent movie) God actually freakin' die and Mankind live on without Him (and without Satan for that matter.)