Who knows what happened after the megaflare at the end?

Perhaps after the devestation of that blast and Mor Dhona is basically ruined..again..Bahamut goes against the Empire directly, a battle that lasts several years until they eventually deal a grevious wound to Bahamut causing him to draw back into his own sancturary. If Bahamut went after the Empire and preoccupied them, it would give reason for the 3 city states to focus on rebuilding their own homes and making new fortifications, while preparing for the eventual return of the war against the Empire that's likely to happen.

Bahamut's Labyrinth could infact be his own domain, somewhere up in Draconia that hasnt been mentioned before, where the original Dalamud was erected around him and cast up into the skies. So we return to the world, five years later, just to come back as the last touches to the 3 city states has come to completion, marking annivesary to the Meteori crisis (which I'm sure they probably would do some sort of grand event in game to commemorate this affair..if not yet planned SHOULD BE) and also in time to start repelling the Empire's assaults as they attempt to take seige over Eorzea again.

Its reasonable. Bahamut is being portrayed as a King of Primals essentially and the Empire despises and wants to eradicate the Primals completely, so them going head to head is to be expected. It would also make sense if they did it this way and make the Imperial controlled lands inaccessible at time of launch because now They need to rebuild while we return to that timeline and start attacking the Primals and Bahamut himself.