And what ever happened to Alph's sister? She just kind of disappeared. The main story really doesn't explain anything. It is like the world ending horrible apocalypse was really more of a minor inconvenience as somehow in the subsequent few years everyone and everything recovered and Bahamut was bound. Even though no one remembers anything. For some reason.

The players were teleported ahead, Lou died, but somehow all the faction leaders and Gaius were perfectly fine when Bahamut Limit Broke.

Dunno. Makes no sense. But Japanese game stories never really make sense anyways. Remember FFVIII?