Eventually, Anders decides to force the Templars' hand and, with or without Hawke's help (albeit unknowingly), orchestrates a massive explosion that levels the Kirkwall Chantry and kills Grand Cleric Elthina, to whom the Templars bear allegiance.
As he concludes his story, Varric reveals that Hawke's companions eventually drift apart and Hawke either disappears during his/her time as Viscount, or leaves Kirkwall soon after killing Meredith (if Hawke had a love interest, that person leaves along with Hawke).