My guess. We have to go into the Antitower to get some Antimatter before Niddhogg so that he can use it to blow up Ishgard right as they cave in to that new cult and vote for a new bishop, like that Dan Brown book with poorly researched facts and the setting being the Vatican
Along the way We'll have to fight the Antichrist, find some Antifreeze, use Godbert's stash of Anti-aging cream and help a brooding Anti-hero along the way throgh the Antitower.
Okay Serious guess time. I think that the tower might either be sticking out form benith Azys Lla or the Sea of Clouds. or is just a fancy term for an underground building, much like Pharos Sirius HM, we start at the top and must work out way down.
Also in keeping with the trend established with Wanderer's Palace HM, Neverreap and Pharos Sirius HM, Lost City of Amdapor HM will have a plot of helping or foiling rouge beastmen (Base don the location Sylphs are most likely, but in spite of being "headquartered" in Coerthas, the Ixal are another likely choice for their enmity to Gridania)