Two Years Later,Jak is injected with Dark Eco. Daxter finds Jak and freed him. After they escape,Jak and Daxter met Kor and the Kid. The Krimzon Guard tried to recapture Jak,but he transform 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 and his bodyguard,Sig. Jak begun training with Guns. Jak and Daxter seeks out Vin,a paranoid scientist,and Ashelin,a high-ranking member of the Krimzon Guard who works with the Underground. Jak begun practicing racing.
Later,Jak and Daxter overheard Praxis and Errol talking to the Metal Head Leader and that Ashelin is the Praxis' Daughter. The two went to the Sacred Site,outside the walls,where they found Samos's hut which is now overgrown and realized that they're in the future. The Two met the Shadow,who turned out to be a Younger Version of Samos.
They met the Soothsayer,Onin and her Moncaw named Pecker,who assigns them to find three special artifacts and destroys the Baron's Statue,revealing the Tomb of Mar and its guardian,an oracle. While there,Jak and Daxter finds the hidden Precursor Stone. The Baron arrives and stole the Stone,capturing Samos,the Kid,and Kor.
Jak and Daxter manage to find Young Samos and Tess,the member of the underground who spies on Krew. They even found the Samos they knew. They reunite with Keira,who was working at the stadium. Samos sends Jak and Daxter to find the Life Seed at the Old Hut to give it to the Young Samos. Jak begun racing with Erol at the Stadium and wins. Praxis recognizes Jak and orders the guards after him. Erol tried to run him down,but he misses and crashed into a crate of Dark Eco.
Jak and Daxter 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 and left Krew to die in the explosion. Jak and Daxter confronts Praxis and his Guards before they encounter Kor,who reveals himself as the Metal Head Leader. He kills Praxis and leaves. They recover the Stone.
They arrived at the Metal Head nest to confront Kor,who reveals that the Kid is a younger version of Jak. Jak transforms and battles Kor. After being weakened,Kor tried to fly to the Rift Gate,but gets blowned and killed. Samos and Keira arrive to send Young Samos and 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 renames it "the Naughty Ottsel"(since after Krew's death) and watch the Fireworks in the sky.