I don't think the Ul'dah plot will be after the battle of Ishgard but before. I think the cup is some kind of holy grail ( related to the 12 knights of the round of Ishgard maybe ) and not to Ul'dah. Then we don't know what would happen but it would be unlikely to have Lolorito take control of Ishgard.

Then for the crazy Theory speculations : Yugiri reveal she is half dragon to try to stop the battle of Ishgard and manage to rally Ishgardians and heretics to stop the battles, the dragons keep attacking but are driven back, the pope is freed from the ascians' control and thus makes a shift in the power in Ishgard, Aymeric takes control of Ishgard and try to open Ishgard, make peace with the dragons ( some accepts thanks to Midgardsommrs but most refuses and want even more blood )and the heretics.