This new quest will appear after All That Remains is done.
Upon examination of your Writing Desk at Hawke Estate in Hightown, you will find that the Viscount has written to you, urging you to meet him as he has an urgent personal matter which he will share with no one but you. Travel to the Viscount's Keep (in Hightown) to meet him.
He explains that his son Saemus has decided to convert to the Qun. He fears that that the Qunari are using Saemus to trigger the political crisis that has been brewing ever since they arrived, saying that at best his opponents would accuse him of letting the Qunari influence his office, and that at worst he would lose his son.
Travel to the Docks to have a word with the Arishok. While traveling there is a random encounter with a couple of Thugs and Mercenaries. Between you and the thugs is a standard trap (20 cunning to detect and disarm - 100 XP). Take the Cowl of the Overseer or the Helm of Enasalin or the Stonehammer Helm, depending on your class from one of the bodies. Continue to the Docks to reach the Qunari compound (note there's a crate hidden next to one of the exits to the Qunari Compound as well as a barrel in a corner of the room). The Arishok tells you that Saemus has converted of his own volition and his relationship with the Viscount is irrelevant to them. He adds that a letter preceded you to arrange a meeting with Saemus, and he suspects foul play from Petrice. Saemus has been lured to the Kirkwall Chantry at Hightown in the night.
You may visit the Viscount and warn him that Saemus is seemingly in danger from the Chantry, but he protests that he cannot be seen to be putting pressure on the Chantry, even though they lean on him. Rather than sending the Guard, he asks you to save Saemus.
At the Chantry, after the shocking cutscene, you will face Petrice's supporters. They aren't very tough, but you may want to focus your fire on the Mob Leader. IMPORTANT: if you want loot, make sure that you collect before the battle ends, because a cut-scene takes over.
If you supported Ser Varnell earlier, and you pick the option to help Petrice frame the Qunari for Saemus's murder, a group of Qunari will enter the Chantry saying that they knew the Arishok should not have trusted you; you will have to fight them instead. If you do so, Petrice will not be killed by a Qunari assassin, but Elthina will strip Petrice of her title. This results in Aveline: rivalry (+10).
Watch another cutscene, after which you will be sent outside the Chantry.
If you had sided with Mother Petrice, she will be waiting for you outside the Chantry. Speaking to her and asking for her support (diplomatic option) results in Aveline: rivalry (+5) and Isabela: rivalry (+5).
- 3 and 1000 XP(quest completion, after the cut-scene).
- The History of the Chantry: Chapter 3 is only available during this quest. It is located on the podium near to where you start the fight. It is required for the achievement 'Chantry Historian'. You will need to acquire it before the fight ends. It's in plain sight but hard to target. The best way to view it is to pause your game with the radial menu until the eye is visible and repeatedly click on it.
- If your Hawke has humorous personality, go to the Chantry alone, without any companions in the party. After the last cutscene Hawke walks out of the Chantry and delivers a hilarious monologue. 
- Under some circumstances (using the diplomatic choices) when you first talk to the Arishok the whole conversation will start over. (Confirmed). (May Relate to the Shield Glitch).
- Under some circumstances (using the humorous/sarcastic choices) when you finish talking to the Arishok the whole conversation will start over.
- Under some circumstances (using the aggressive choices) when you finish talking to the Arishok the whole conversation will start over.