I actually thought of this when I read the Bahamut description a while back. There was no mention of Louisoix's death. Even in-game they spoke of him as "gone", but never did they outright call him "dead". This is a rather obvious buildup to his return.

SE still has the ability to shock us with it, though. Maybe he's locked in extra-dimensional combat with Bahamut. Maybe he lost the extra-dimensional battle, allowing Bahamut to return to our world five years later. Maybe he's FUSED with Bahamut (I'm feeling a little macabre right now.)