'X' aka 'Xavier' in Fantomex's body aka Deus Ex Machina solves everything (or maybe not really?).
Soule restores Warren to basically the same state he was in the end of Bunn's Uncanny run (or not?)
Fantomex's mind is now trapped in the astral plane as a result of offering his body to Xavier (but maybe he was manipulated into doing it?)
Bishop discovers that an event called "mindkiller apocalypse" could be coming.
Proteus comes back as a result of Xavier's ressurection.
Also Fantomex's face looks pretty much like a younger version of Xavier which is I guess the result of some sort of reality manipulation or just an incredible coincidence.