Jak and his Daxter went to Misty Island,which Samos forbids them not,where Daxter was accidently send into a pool of dark eco. He emerges transformed into an Ottsel,unharmed.

At Sandover Village,They seek help from Samos. He explains that the Dark Sage,Gol Acheron,who lives far to the north,can reverse the transformation. Samo's Daughter,Keira,who was interested in Jak,tells them to the North,They could use a Zoomer as an exchange for Power Cells.

After collecting Power Cells,Jak and Daxter make their way through the Fire Canyon to Rock Village,the home of the Blue Sage. The Village has been attacked by a Lurker,Klaww. Jak and Daxter collect more Cells and help Keira clear the path with the levitation Machine so that the Boys can defeat Klaww.

Jak and Daxter cross the Mountain Pass and made it to the Volcanic Crater where the Red Sage dwells. At this time,the truth is revealed: The Blue,Red,and Yellow Sages have been abducted by Gol and his Sister Maia,the figures that Jak and Daxter saw on Misty Island. Their Goal is to open the Silos containing the vast of dark eco so that it could destroy everything it touches.

After getting more Cells,Jak and Daxter arrived at Gol and Maia's Citadel,Where Keira reveals that Samos has been captured. Keira wishes Jak to be careful,hugging him. The Boys freed the Sages,But the Acheron Sibling piloted the Precursor Robot to the Silos.

Jak and Daxter battled them. The Sages combined their eco into one,Light Eco,which Daxter believed this could change him back,but decide to let Jak use it to destroy the robot. The Head of the Robot with Gol and Maia inside plunged into the silo. The Sages congratulates the boys. Keira gave Jak a kiss. Jak and Daxter has 100 Power Cells to unlock the fabled Precursor Door. Once it opens,it is reveals a large,mysterious object enveloped in a blinding light.