Since this topic isn't tagged for spoilers:
Clearly the Ascians are orchestrating everything going on in Ishgard. For how long this has been going on, who knows? It's pretty clear now why the Ishgardians refused to join the Eorzean Alliance during Dalamud's descent though. I'm not so sure the Ascians have a direct hand in the heretics. (which seems to be a pretty general term, since Shiva seems to be controlling some, while there are others who appear to side with dragonkind. I think "heretic" is anyone that doesn't abide by the Papacy)
After mulling this over, if the Ascians have this sort of influence over people such as an Ul'dahn Syndicate member and the holy leader of a nation, why haven't they tried to interfere with the other nation leaders? Is it because the adventurers and Minfilia are in such constant contact with them that we would eventually see through their ruse?