After Gol & Maia's defeat & discovering the mysterious object,Jak & Daxter join Samos and Keira testing an ancient artifact known as the Rift Rider. After Jak activates the device,The Gate opens,allowing the creatures to flood the world before they're being sucked into it. Jak & Daxter become separated from the others and ended up in Haven City,ruled by Baron Praxis. Jak gets knocked out by the Krimzon Guard led by Errol,Praxis' right hand man.
Two Years Later,While Jak is injected with Dark Eco,Daxter finds him. After they escape,Jak & Daxter met Kor & the kid before the Krimzon Guard tried to recapture Jak,but he turns into a Dark Eco version of himself,killing them. Kor explains the Underground,a resistance movement led by the Shadow,seeking to bring down Praxis. The two met the Shadow's Lieutenant,Torn,a former Krimzon Guard,who tells them the Baron is seeking to protect the city from the Metal Heads,an evil biomechanical race dating back from Precursor times.
Torn sent them to the Hip Hog Heaven Saloon where they met Krew & his bodyguard,Sig. Jak begun training with guns. The duo seeks out Vin,a paranoid scientist,& Ashelin,a high-ranking member of the Krimzon Guard who works with the Underground. Jak begun practicing ,Jak & Daxter overheard Praxis & Errol talking to the Metal Head Leader & learned that Ashelin is the daughter of Praxis. The two went to the sacred site,outside the walls,where they found Samos' hut which is now overgrown & realize that they're in the future before they met the Shadow,who turned out to be younger version of Samos. They met the Soothsayer,Onin & her Moncaw,Pecker,who assigns them to collect three special artifacts & destroys the Baron's statue,revealing the Tomb of Mar & its guardian,an Oracle. Jak & Daxter finds the hidden Precursor Stone,but the Baron arrives & stole the stone,capturing Samos,Kor,& the Kid.
The duo manage to find Young Samos,Tess,the member of the underground who spies on Krew,& the Samos they knew. They reunite with Keira,who was working at the stadium. Samos sends Jak & Daxter to find the Life Seed at the Old Hut to give it to the Young Samos. Jak begun racing Errol at the Stadium & wins. Praxis recognizes Jak & Errol tried to run him over,but Jak jumps out of the way & Errol crashed into the crate of Dark Eco.
The Duo confronts Krew,who reveals the piercer bomb,which has the power to destroy the Precursor Stone. After Krew gets defeated,He activates the self destruct system. The two escape with Ashelin,leaving Krew to die in the explosion. Jak & Daxter confronts Praxis before they encounter Kor,who reveals himself as the Metal Head Leader. He kills Praxis before Jak & Daxter recovers the stone.
They arrive at the Metal Heads nest to confront Kor,who reveals that the Kid is a younger version of Jak,who was hidden in the past. Jak transforms & battles Kor,weakening him. Kor tried to escape to the Rift Gate,but gets blowned & killed. Samos & Keira arrives to send Young Samos & Young Jak to the past,so they may prepare everything for the present.
Ashelin became the New Governess as the group prepares to celebrate at the Saloon,which Daxter renamed it the Naughty Ottsel & watch the Fireworks in the sky.