In Sandover Village, Jak, Daxter, Keira and Samos activate the mysterious Precursor Ring recovered from Gol's citadel using a Rift Rider vehicle. This triggers the emergence of monstrous creatures, including a massive beast searching for a "boy", forcing the group to flee through the Ring. The Rift Rider explodes, separating Jak and Daxter from Keira and Samos, and they crash-land 300 years into the future in Haven City, a dystopia ruled by the tyrannical Baron Praxis. Jak is captured by Praxis'
police force, the Krimson Guards, and for two years he is subjected to brutal experiments infusing him with a substance known as Dark Eco. The experience transforms Jak into a
vengeful figure capable of becoming Dark Jak. Daxter, after evading capture, infiltrates the fortress to rescue Jak, who breaks free using his new powers. In Haven City, Jak and Daxter encounter Kor, an old man with a mysterious green-haired boy, who informs them of Praxis' oppressive rule and directs them to the Underground, a resistance group commanded by former Krimson Guard Torn and led by the Shadow (later revealed to be a younger version of Samos). After proving their loyalty by stealing Praxis' banner from Dead Town (the ruins of Sandover Village), Torn tasks them with missions that undermine the Baron, such as restoring water to the
slums. During a mission to destroy an ammunition depot, they discover Krimson Guards supplying Dark Eco to Metal Heads, the creatures that attacked Sandover Village. Through Torn, the duo meets Krew, a shady
saloon owner who supplies the Underground with weapons and hires the two for tasks like eliminating Metal Heads and retrieving
artifacts. Krew reveals Praxis' arrangement with the Metal Heads, in which Praxis exchanges Eco for controlled Metal Head attacks on the city to justify his regime. Jak and Daxter also meet Ashelin, Praxis' daughter and a conflicted Krimson Guard member, who is investigating her father's search for the
tomb of Haven City's legendary founder Mar. The tomb holds the Precursor Stone, a powerful artifact that Mar hid from the Metal Heads, the ancient enemy and destroyer of the Precursor civilization. Praxis seeks the Stone to solidify his power, while the Metal Heads, led by their Leader (the large creature that emerged from the Ring), aim to consume its energy. Meanwhile, Jak reconnects with Keira, now a
mechanic and racer, who is building a new Rift Rider to return them to their time. To locate Mar's tomb, Jak and Daxter work with the blind and mute
soothsayer Onin and her monkey-
macaw hybrid interpreter Pecker, who task them with recovering artifacts that lead to its location. Within the tomb, Jak passes its tests of manhood, but Praxis, having followed him, makes off with the Precursor Stone. Ashelin informs him that Praxis and Krew are meeting at a
weapons factory, where they are preparing to use a Piercer Bomb to crack the Precursor Stone open and release the energy inside. Jak and Daxter defeat the treacherous Krew and recover the Heart of Mar gemstone, a key component for Keira's Rift Rider, before leaving Krew to be caught in the Piercer Bomb's explosion. The city falls under siege as Kor reveals himself as the Metal Head Leader, having manipulated events to access the Stone. Praxis, mortally injured by the Metal Head Leader, reveals to Jak and Daxter a second Piercer Bomb with the Precursor Stone attached, and Daxter disarms the bomb to secure the Stone. In a final confrontation at the Metal Head nest, the Leader reveals that the boy is Jak's younger self, who was born in Haven City and sent to the past to gain the strength needed to defeat him, and that the Stone houses a Precursor entity that only young Jak can release. After Jak defeats the Metal Head Leader, young Jak releases the Precursor entity, which declares the Precursors' war against the Metal Heads over and tells Jak that his Dark Eco corruption has been balanced with light. The young Jak and Samos are sent back to the past to fulfill their destinies, while the Precursor Ring is destroyed. Ashelin becomes Haven City's governor, and Torn leads the reformed Krimson Guards. Daxter rebrands Krew's saloon as the Naughty Ottsel, where the group celebrates their victory. Jak reflects on his younger self, and Samos hints at future adventures involving Mar. == Development and release ==