Jak, along with Daxter and Pecker, were taken into Damas' sanctum where they were bathed and Jak's clothing was reduced and his hair cut. Jak nearly died, as Damas noted he was preparing to have his pray for him. Jak fought in arena matches to prove himself worthy of keeping, where he eventually earned citizenship to Spargus, and became an official "wastelander." During this process he met again, an ally from , in the , where they were ordered to kill each other under arena rules, though they both withheld the task and were forced to prove their worth to Spargus another way.
From then on, Jak worked with a variety of new characters including , a local smuggler and gang-lord, who had apparent connections with the Underground, as well as , a blind soothsayer who knew of Jak's arrival from the past, and was also able to foresee his future. Others included , , , and . Jak later discovered that the strange new world which they were making their way through was actually in the future, and that Haven City was built around Sandover Village, which was now known as .
Throughout the course of the game, Jak completes missions acquiring coordinate spheres which activate the seeker. Eventually Jak discovered that the Aeropans were conducting a Dark Warrior Program on their citizens, making him angry and vengeful, where he then joined the previously antagonistic Sky Pirates in an effort against the Aeropans. In a siege on Aeropa, Jak finally met up with Skyheed, who also turned into a massive Dark Warrior.
After being rescued by Daxter and escaping from , Jak experienced the first display of his (evinced from past experiments) while defeating a squad of guards in the . He was asked to do so by —who was disguised as a human working for the Underground—in order to protect a "very important" child. After defeating the guards, Kor directed Jak to the Underground, a rebel movement waging war against Baron Praxis; Kor noting that its leader, the Shadow, could use fighters like him (Dark Jak). Kor told Jak to find the hideout in a dead-end valley near the city wall, instructing him to ask for . Upon meeting Torn, Jak was at first rejected. After Jak told the leader that he wished to see the "Shadow," Torn gave him the mission "", in which Jak succeeded; starting initiation missions for membership to the Underground.