This new quest will appear after All That Remains is done.
Hawke Estate Edit
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.
Viscount's Keep Edit
He explains that his son Saemus has decided to convert to the Qun. He fears 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.
Winding Alley Edit
Travel to the Qunari Compound at the Docks to have a word with the Arishok. On the way there is an ambush with a small group of Thugs and Mercenaries at the Winding Alley, with a similar layout to the Disused Passage only using the southern entrance/exit section. Between you and the thugs is a standard trap (20 cunning to detect and disarm - 100 XP). Take the Act 2 signature headgear (exact item depends on class) from the Thug Leader's remains.
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.
Leaving the Winding Alley deposits you right outside the Qunari Compound, at which point you are free to resume exploring Kirkwall normally.
Qunari Compound Edit
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 (visiting the Viscount is not required for this quest and has no change on the outcome).
The Chantry Edit
At the Chantry, after the shocking cutscene, you will face Petrice's supporters. They're all Critter-ranked, but you may want to focus your fire on the Mob Leader, an Elite-ranked Templar-type Commander, or at least keep him stunned while you put down the rest of the mob. The Righteous Mob mixes fire immunity/cold weakness on its melee enemies and cold immunity/nature weakness on its archers.
It is possible to defeat them on Nightmare by yourself, which results in a hilarious rambling monologue from a Sarcastic Hawke upon exiting the Chantry. It may be an exercise in patience and kiting, however, as the Mob Leader resists most low-grade stun effects like Miasmic Flask and as a result keeps his healing aura up for a long time. This results in the Critter-ranked mob being able to heal faster than they can be slain by a solo Hawke. Dual-wielding Hawkes should switch to archery and keep a healthy distance, running around the upper walkways of the Chantry. The first priority should be the archers (there's only a few in total across two waves), taking them down with whatever burst damage technique you have (Punishing Lance for a dedicated archer works perfectly here, but Assassinate and Vendetta also work nicely), then kite the remaining enemies and attempt stuns for as long as it takes. Mages should have Horror or Petrify to stun the Mob Leader regularly, and warriors should be able to cut through them with Cleave, Destroyer, and Massacre, as well as their activated talents of choice.
- If you want loot, make sure that you collect it before the battle ends, because two cut-scenes take over and force you out of the Chantry after the second one. Also, be sure to grab Codex entry: The History of the Chantry: Chapter 3 before the cut-scene, because this is your only chance to get it; see information under Rewards below. It is essential for the Chantry Historian achievement/trophy.
Alternatively, an Aggressive Hawke could have supported Varnell during Offered and Lost then agreed to help Petrice frame the Qunari for Saemus's murder. If you do so, a group of Qunari lying in wait will enter the Chantry, saying they knew the Arishok should not have trusted you, and you will have to fight them instead. This results in Aveline: rivalry (+10).
The following scene depends on the outcome of the battle: If you fought the Righteous Mob, then Petrice arrives with Grand Cleric Elthina and attempts to pin Saemus's death on Hawke and the Qunari. Elthina instead implies that she knew what Petrice was up to all along, that recent events have proceeded as she predicted "all too well." Elthina hears Hawke out, and all dialogue options lead to exposing Petrice. Elthina strips Petrice of her title, informing her she'll be brought before the court and tried for her actions. As the Grand Cleric heads back upstairs, Petrice is shot through the heart by a Qunari archer, forgoing the need for a trial. No other Qunari arrive and you do not fight any Qunari in the Chantry.
If you fought Qunari, Elthina will confront Petrice later, outraged at and fully aware of what she's done, that recent events have proceeded as Petrice predicted "all too well." The Grand Cleric strips Petrice of her title, however the former Mother won't be assassinated by the Qunari.
In the next cutscene, Viscount Dumar arrives and mourns over Saemus's body, asking what hope there is for the city when it fails its own like this. If you choose the humorous option ("It can't get any worse. Not today at least, it's getting late"), and Aveline is in the party then Aveline: rivalry (+5). Aveline will call Hawke an "ass" for this remark outside.
If you had sided with Mother Petrice, she will be waiting for you outside the Chantry. Speak to her:
- diplomatic option: Anders: rivalry (+5), Aveline: rivalry (+5) and Isabela: rivalry (+5).
- aggressive option: Anders: friendship (+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 a 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 monologue. 
- Under some circumstances, when you first talk to the Arishok the whole conversation will start over. (May Relate to the Shield Glitch) [confirmed in Xbox360 || only happened once after original conversation]