After bidding goodbye to his friends, Jason heads to Vaas' pirate base. Believing that Jason was dead after a confrontation between the two, Vaas is observing Jason's death, although it transpires he was really waiting for him. After Jason kills numerous pirates and reaches a warehouse, he and Vaas struggle, but Jason enters a delusional state, fighting multiple copies of Vaas in a dream. He reaches a final Vaas, and after a brief struggle, impales him through the chest with the Dragon Knife and collapses directly beside him. He wakes up to Citra from the Rakyat's temple, and promises to kill Hoyt for her.
After Huntley helps him enter Hoyt's island, Jason infiltrates Hoyt's personal army with the help of Sam Becker , Huntley's fellow operative. In this time, Jason discovers that Riley was not dead as led to believe, but a captive of Hoyt. Jason works his way into Hoyt's confidence, who invites him Becker to a poker night. After building a plan to kill Hoyt, Jason and Becker sit down in the poker game, but Hoyt, conscious of their duplicity, fatally stabs Becker in the throat. Jason engages, defeats, and kills Hoyt in a knife fight, losing half a finger in the process, and ultimately rescues Riley, although not before receiving a call from Liza which is quickly cut off.
As outposts of Vaas' pirate group are assaulted and retaken, the vicinity around the outpost becomes safer and new side quests are unlocked for that region, involving assignments like searching the many different wildlife species on the island to update one's equipment.