By the looks of it, a pretty brutal and direct attack on the part of the Eorzean Alliance and their new allies is going to be how they reclaim Ala Mhigo and Doma. That's assuming they even succeed or that they don't just cause their opponents to destroy the place in an effort to prevent them being claimed by another party. I do wonder, though - what if the flooding of Doma is something inflicted by the actions of the Warrior of Light and his allies? I can't shake the feeling that the Eorzean Alliance is going to go too far somehow, especially since it is directly meddling in the affairs of foreign nations.
It's the events at Baelsar's Wall that make me fairly certain that this is going to be the case, along with the lyrics of the song in the trailer. Furthermore, Ishgard made it crystal clear that the Warrior of Light and his allies have no issue slaughtering those who just happen to remain loyal to a cause that they oppose. How many of those murdered in The Vault, for instance, were cut down without ever being given an explanation of the Archbishop's true plans? How many of those slain had friends and family who are left hollow as a result? Forced to see their loved ones branded as the 'bad guys' by those who engage in desperate virtue signalling to be seen as 'progressive'?
It reminds me of how FF7 took measures to show that the protagonists, in all their self righteousness, engaged in terrorist attacks that caused innocent people to die simply because they happened to be associated with Shinra, an organisation that employed countless regular workers rather than just soldiers. What will the Warrior of Light and Scions do if, in their attempt to reclaim territory, a bunch of non-combatants decide to defend their friends and family with pitchforks? Will they be cut down if they can't be convinced? All excellent questions and scenarios I hope the developers take into consideration. I have faith that they will given the trailer's content and lyrics, though.
It'd be interesting to see how a lot of the people frequenting this place would react if the reality of such a war was explored in full.