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I counted three seperate occasions when the game announced "A=B, and B=C" and yet people seem confused about the relationship between A and C. Two of the Intrigue for Dummies equations were spelled out in the last level. Do people really wonder who #1 is, or is it fannish petulance because the answer isn't skywritten in neon letters?

As for what happens next, I don't know if the game is XIII canon, but, um, what do you THINK happens next? Really? Two options: deus ex machina, or what a REAL James Bond villain would do. Seriously, assuming the hero isn't Neo in the middle of the burly brawl, how exactly do you think it works out? Even Jason Bourne would have trouble leaving the room and going topside to watch the fireworks.
The game is actually based on a comic, so you could always dig around for that if you want to know what happens next. I'd prefer to leave it how it is but they could easily have done a sequel.