Being banished into the wasteland by the Tyrannical Count Veger for crimes against Haven City,Jak wonders through the desert with Daxter & Pecker before losing consciousness. They're being rescued by the Desert-Dwellers,led by Damas,King of Spargus. Jak proves himself as a warrior in both the Arena Challenges and by serving the city.
Jak & Daxter befriends with Seem,the Precursor Monk,& Kleiver,the Buggy Garage owner. The duos recover the citizens & artifacts during the sandstorm while racing both Buggies and Leaper Lizards for upgrades,solving puzzles for Eco crystals,catching Kanga rats upon Leaper Lizards. Jak is bestowed with Light Eco abilities to balance the darkness. Jak is found by Ashelin & Sig,learning that Count Veger has been involved with the Deathbot leader. A Precursor Telescope in the outskirts of Haven City reveals that the beings are Dark Makers,who were once Precursor,but exposures to Dark Eco transformed them into twisted beings.
Jak notice that a purple star in the sky is actually a Dark Maker Space Ship & getting closer. After taking out the Metal Head & the Deathbots,Jak & Daxter went through the catacombs to the Planet Core. Damas joins them as they burst through the destroyed section of the city searching for the core. Damas is crushed underneath the buggy. Before dying,Damas tells Jak to find his lost son,Mar and gives him the amulet bearing the seal of Mar to identify him. Jak realized that Damas is his father and Veger comfirms it,revealing that he was taken away from Damas after Baron Praxis banished him before taking over Haven City.
Jak follows him to the core and beaten him. The Precursor entity tells Jak that he has earned the right to evolve. However,It is revealed that the Precursors are actually Ottsel,who turned Veger into one as punishment for his actions. Jak & Daxter went inside the Dark Maker Ship where they confronted the Deathbot Leader,who turned out to be Errol,a former Krimzon Guard commander survived the explosion at the race & is now Cybernetic. As they fight with him, the planetary defense system charges,destroying the ship,but Errol flees in a Dark Maker Robot and head straight to Haven City. Jak follows and destroys the Robot,killing Errol.
Back in Spargus,Sig became new leader. The Precursors gave Daxter pants & turns Tess into an Ottsel. Jak departs with the precursors to see the universe. After the ship takes off,Jak emerges from the shadow and tells Daxter that he's not going anywhere.
Mid-Credits:
Strange beings hovers over the crash site and found half of Errol's body