I feel like there's a message I'm supposed to be seeing here, but alas. Something about messianic figures and the nature of mankind is what I'll go with. It feels like there was supposed to be a few more chapters between the ones we got. Spy girl downright disappeared.
I suppose I'll just be happy with the last-minute return to the eternal battle for humanity's survival. I can always appreciate that sort of stuff. I liked the whole 'quixotic struggle against the suffering of existence' theme of the story a whole lot more than the other stuff.
All in all, I've seen worse endings.