Big time spoiler:
At the end of 3.0 "The Eorzean Alliance is now whole with the inclusion of Ishgard. "let us defend eorzea from the Garlean Empire."
Since the emperor is at the front, seeing to the empire's efforts personally, whether its eorzean conquest or just an expedition to recover more powerful Allagan artifacts, i see the Alliance clashing with the Empire to prevent known but still buried war machines like omega-weapon from falling into the wrong hands.
Now that the Alliance is whole, after repelling the coming invasion, the Alliance will take on an offensive counter-attack to remove Garlean troops from the continent, what better way to start than liberating Ala-Mhigo?
Though this is a long shot, the Empire has set its foot hold and turned able bodied men and women of Ala Mhigo, that didn't flee, into conscripts. When new generations of a conquered country grow up under this, it becomes accepted as the resentment from the suffering generation die out over time. Essentially we will be fighting Ala-Mhigans to recover Ala-Mhigo.
It's been made clear that the Warrior of Light's main purpose is the eradication of Primal entities. So if we are heading into Ala-Mhigo it will most likely be related to Ala-Mhigo refugees being mislead by Ascians into summoning a Primal and taking the war into their own hands.