Alright,
Saji finally hits the "step up and become badass or die wimpering" point and decides to change the world because he's that fed up with the shit happening to him.
At one point or another, he goes head to head with Louise and nearly kills her, but then remembers that he loves her more than his own fucked up life and runs off. Louise, on the other hand, gets a face full of GN particles, AND IS COMPLETELY UNHARMED...physically atleast.
Thus, Loise starts to wonder, "was it really CB that killed my parents?"
Somewhere along the line, Al and Marie elope and live happily ever after, until the inevitable sequel/spinoff, that is.
Setsuna eventually blows Ali away with an RPG-7 while on foot. Starts calling himself Soran again, tells Saji to take his place, and gets caught in the explosion of the final battle.
Some time later, a masked bodyguard is hired by a politician named Marina Ismail.
A mission to colonize the stars starts to gain momentum.
"Just as planned."
-Aeolia Shhenberg