Disobeying the village Sage, Samos, you explore a forbidden island off the coast and find some Precursor ruins. You decide to investigate, but while inside the mysterious buildings a terrible accident occurs, when you knock your friend Daxter into a huge vat of dark sludge transforming him into a weasel-like rodent.
Samos the Sage realises that your friend has been exposed to Dark Eco, a rare and dangerous substance left over from the creation of the universe. The only way to change him back is to trek far North to find a fellow Sage named Gol Acheron. Being the only Sage studying Dark Eco, he may hold the secret to undoing your friend’s transformation.
You begin the harrowing journey north, with the help of your Mentor and his mechanically savvy daughter, Keira. Along the way you learn more about an ancient race called the Precursors and about your unique ability to control Eco, the naturally occurring energy of the world. Ultimately, you expose a plot by a Dark Eco corrupted Gol and his evil Sister Maya to kidnap the four Sages of the land and force them to piece together a giant Precursor robot. Using this robot, they plan to unleash vast underground stores of Dark Eco, twisting the world forever.
Intent on stopping this plan, you battle your way to Gol and Maya’s lair in an underground Precursor City, arriving just as the kidnapped sages are putting the finishing touches on the evil Robot. As you prepare to destroy the robot, Gol and Maya, launch it into action, escaping before you can deliver your death blow. You chase after their mechanical monstrosity down twisting subterranean passageways until you have them cornered, where you battle it out to save the world.