Uhhh... the short of it? Kirkwall Circle was super bad, oppressed the mages to the point where an apostate blew up the Chantry to kickstart a battle. Lot of people died. [It's drastically simplifying it, but even Prompto doesn't know everything.] The knight-commander of the Templars called for an annulment of the Circle - meaning they kill every mage in there. They all had to fight for their lives and flee.