The Arishok and his Qunari were pursuing Isabela, who had stolen the Tome of Koslun as Orlais attempted to return it to the Qunari. During their sea battle, Isabela's ship was sunk by the Arishok's forces, while a storm shipwrecked the Arishok, stranding both parties in Kirkwall. The Arishok and his forces then set up a base in the docks of the city lent to them by Viscount Marlowe Dumar as a peace offering.

During Act 1, a dwarven merchant named Javaris Tintop sought to buy the formula to create gaatlok, a Qunari explosive powder, from the Arishok, but was refused. As a result, Javaris attempted to broker a deal with the Arishok to slay Tal'vashoth in exchange for the formula, and hired Hawke to do the job for him. When he returned to the Arishok, the Arishok refused him again, stating first that the Qunari had never agreed to the deal and second that Javaris had not done anything; it was Hawke who had done the deeds. Later, the Arishok dispatched warriors led by an arvaarad in search of a saarebas. The saarebas' karataam had been slain by Tal'vashoth, and according to the Qun, he had to be killed, as he had existed for a time without oversight. The karataam encountered Hawke, who had been leading the saarebas at the behest of sister Petrice - she had hoped to have the Qunari kill Hawke and her friends, allowing for an excuse to lead an insurrection against the Qunari. However, they were all killed by Hawke, but the saarebas died as well. When the Arishok learned of this, he stated simply that Hawke's actions were impressive, and the important thing was that the saarebas had been slain. When informed that a sister was attempting to cause conflict between him and the city, he was unconcerned as well.

By Act 2, tensions began to grow between religious factions, as some citizens of Kirkwall began to convert to the Qun. The Arishok himself had long been irritated with the chaos and corruption rampant in the city, and had even mentioned to Hawke that the Qun might eventually demand that he step in to "enlighten" the people of Kirkwall. In Blackpowder Courtesy, the Arishok requests Hawke's presence. When Hawke arrives, the Arishok informs them that someone has stolen the formula for saar-qamek, a poison gas that drives non-kossith insane before killing them. The culprit had been attempting to steal the formula for gaatlok, but the formulas were switched in order to lure the Qunari's enemies out of hiding; the Arishok suspected that it was Javaris, since he was the only person who had attempted to buy gaatlok and had not accepted "no" for an answer. Hawke eventually discovered the culprit was a deranged elf who hated the Qunari for converting her siblings, claiming elves were losing even more of their culture. When brought to the attention of the Arishok, he was unconcerned, stating that their enemies were too cowardly to outwardly confront the Qunari and that his task was not to convert the city.

Eventually, the Arishok was provoked to the point of retaliation when three events occurred that he could not ignore. Saemus Dumar, son of the Viscount, converted to the Qun and was murdered by mother Petrice, who had set up Hawke long ago. At the same time, the city guard began petitioning the Qunari to extradite two elves who murdered a corrupt city guard and converted immediately after, claiming religious sanctuary with the Arishok. Finally, and most important to the Arishok, the Tome of Koslun was stolen once again by Isabela as his warriors attempted to recover it. The Arishok concluded simply that he could not stay in Kirkwall any longer and ignore the corruption and disease of the city, but he also could not leave without the Tome. As such, he chose to correct the corruption, and orders a Qunari attack on the city, nearly killing Hawke and Aveline as they attempt to negotiate with him. The Qunari easily overcome the city guard and seize the keep, with only Hawke, the Templar Order led by Knight-Commander Meredith, and a few members of the Circle of Magi led by First Enchanter Orsino opposing him. The Arishok decapitated the Viscount and gathered all the nobles in the city in the Keep, threatening execution if they did not convert to the Qun. At this point, Hawke broke into the keep.

The following outcomes are possible:

• Isabela returns and hands the Tome of Koslun to the Arishok. He attempts to take her along to Par Vollen so as to convert her to the Qun and to punish her for her actions.
  • Hawke allows the Qunari to take Isabela with them, and they leave Kirkwall without further bloodshed. Varric tells Cassandra that he heard she escaped three days later with the book by jumping into the ocean. Though he states that he does not know if this is true or not.
  • Hawke refuses to allow that and has to confront the Arishok.
• Isabela never returns and Hawke has to confront the Arishok.

See Arishok (strategy) for class-specific strategies for the duel.