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Following the Qun - Introduction
You should pick this one up near the end of the main quest. The Viscount’s son, Seamus, has decided to join up with the Qunari and that’s gone over as well as one would expect. You need to go down to the compound and talk to Seamus and try to get him to come back peacefully. I assume that you have a go-to combat party, so just pick a balanced set and call it a day.
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Following the Qun - Ambush and a Meeting
When you try to go to the Docks, you will be pulled off into a side alley for an ambush by a bunch of thugs. They’re a standard gang of mercenaries, so I don’t think that they will cause your party any real trouble. Just keep your group focused and your ranged fighters protected. Have a tank pull the fighters to them, and pick off the grunts at the edges.
Make sure that you get the helmet off of one of the leader’s bodies. It’s a pretty nice piece of loot.
Once you make it past the gang, go on to the Qunari Compound and talk to the Arishok. He'll tell you that Seamus has already left to go meet with his father, which is an obvious ambush.
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Following the Qun - Finding Seamus
Go to the Chantry at night to find Seamus' body at the altar. Mother Petrice will be waiting for you too. You may have a bit of a decision here. If you decided to kill the Qunari and support Petrice's actions, then you have the option to say that you approve of what has happened.
If you do this, then several Qunari assassins will storm the chantry and attack you. I don't believe that this will be too difficult for most players. Just watch your back and tie them up with a tank. Watch out for any ranged fighters on the edge, and then grind down the rest. It should be like any other fight with the Qunari and end on the unremarkable note that you trick the grand cleric into thinking the Qunari killed Seamus.
If you are against Petrice, then you will have to face her mob. It's actually not that dangerous, if you're alert. The only tough fighter is a templar commander that's acting as a mob leader. The rest are weak grunts. The only danger that they really present is that some of them are armed with bows. You'll need to take them down very quickly if you don't want them to pick away at you throughout the entire battle.
If someone fast can deal with the archers, and a second smaller mob that shows up during the fight, while a tank distracts the templar, then it should be fine. A mage or warrior can use AOE abilities to pick at the templar while tearing away at the rest of the mob. Basic AOE spells will also clear the floor in a hurry, although, the wide area in the chantry will make it hard to bottleneck them.
Once you can grind down the mob leader, it's basically over. Kill any stragglers that you may have missed to trigger the final cutscene. Regardless of what you say to the Arishok, a Qunari assassin will appear and kill Petrice.
The grand cleric will believe you, but won't be able to do much. The Viscount will show up after the first cutscene plays.
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All screenshots from "Dragon Age 2."
All information based on a "hard" difficulty playthrough unless otherwise noted.