Scénario
Like Jak and Daxter: The Precursor Legacy, the game's begins with a speech by Samos Hagai. Jak, Daxter, Samos and Keira are in the process of activating the rift rider, the precursor device hidden behind the large door at the end of Precursor Legacy, and its accompanying rift gate. When the gate is activated a large figure steps out, accompanied by a swarm of creatures. Jak panics and activates the rift rider, propelling the group through the gate. As they are travelling through the rift, the rider is destroyed. The group fall out of the rift and are separated, though all find themselves in Haven City. Jak and Daxter land and are immediately identified by a patrol of the Krimzon Guard, led by Captain Erol. Jak is taken into custody, as Daxter promises to rescue him (see the events of Daxter). Two years later, Jak is in the Fortress, where he has been the subject of a super soldier program. His body has been infused with dark eco. Erol and the Baron Praxis are there. They declare the 'Dark Warrior Program' a failure. They leave, just as Daxter appears to rescue Jak. As Daxter fidgets with the restraints, Jak transforms into the Dark Warrior Program's ultimate goal, Dark Jak. He breaks the binds and then returns to normal, after speaking his first words, "I'm going to kill Praxis!" The pair then escape the fortress into Haven City.
