Jak II (known as Jak II: Renegade in the PAL region) is the second installment (third chronologically) in the Jak and Daxter series, developed by Naughty Dog, Inc. and published by Sony Computer Entertainment. It was released in October 2003 for the PlayStation 2 console, later released in February 2012 and June 2013 for the PlayStation 3 and PlayStation Vita, respectively, as part of the trilogy remaster. Official emulation support for the game on PlayStation 4 was added on December 6 2017, and it was made available to purchase standalone or in a bundle alongside The Precursor Legacy, Jak 3, and Jak X: Combat Racing.[1] It is the first game in the series to drop "Daxter" from the title, with which Jak 3 and Jak X followed suit as well.

Jak II takes on a notably darker tone with a more cinematic story-telling approach compared to its predecessor. While beginning where The Precursor Legacy left off, Jak, Daxter, Keira, and Samos are abruptly thrust into the foreign, industrious Haven City. Jak is captured by the Krimzon Guard and subsequently subjected to torturous dark eco experiments. With his eventual escape, aided by Daxter, Jak is now a wanted fugitive, pumped with dark eco and capable of transforming into a savage alter-eco. Blinded by revenge, Jak joins forces with the Underground and must take the fight to the Krimzon Guard, ultimately becoming entangled in the fate of the cosmos for which he had never been prepared.

Notwithstanding, the core of Jak II's gameplay remains similar to that of The Precursor Legacy, with an identical move set and the recurring reliance upon zoomers and platforming challenges. To add to his moveset, however, Jak is given control of all-new dark powers evinced by the experiments. Also different is a significant amount of gun play to replace various eco powers, the addition of a hover board, and a departure from the usual progression of missions: Instead of collecting power cells, the player now has to complete a set of missions that go from linear to more open, ending with a linear finale.

Like The Precursor Legacy, Samos Hagai begins the game's story with his speech. Jak, Daxter, Samos, and Keira are in the process of activating the Rift Rider, the precursor device hidden behind the large door at the end of Precursor Legacy, and its accompanying Rift Gate. When the gate is activated a large figure steps out, accompanied by a swarm of creatures. Jak panics and activates the Rift Rider, propelling the group through the gate. As they are travelling through the rift, the rider is destroyed. The group fall out of the rift and are separated, though all find themselves in Haven City. Jak and Daxter land in the industrial sector, where they're immediately identified by a patrol of the Krimzon Guard, led by Captain Erol. Jak is taken into custody, as Daxter promises to rescue him (see the events of Daxter). Two years later, Jak is in the Fortress, where he has been the subject of a super soldier program. His body has been infused with dark eco. Erol and Baron Praxis are there. They declare the 'Dark Warrior Program' a failure. They leave, just as Daxter appears to rescue Jak. As Daxter fidgets with the restraints, Jak transforms into the Dark Warrior Program's ultimate goal, Dark Jak. He breaks the binds and then returns to normal, after speaking his first words, "I'm going to kill Praxis!" The pair then escape the fortress into Haven City.

Once outside, they meet an old man and a child. The man introduces himself as Kor. A patrol of Krimzon Guards approach and Kor offers to help Jak if he saves them from the guards. Jak transforms into Dark Jak, and fights off the guards. Per their deal, Kor tells Jak to seek out the Shadow, the leader of the Underground, a resistance movement. When they reach the hideout, Jak and Daxter meet Torn, a high-ranking member of the Underground and their coordinator. He assigns them their first missions and oversees the occasional challenge missions. Torn refuses to let Jak and Daxter meet the Shadow until they have proven themselves loyal to the cause.

On one such mission, while infiltrating the Krimson Guard fortress, they find a group of Krimzon Guards supplying eco to a group of Metal Heads when the two factions are meant to be at war. Torn then sends the "Demolition Duo" on a delivery job to the Hip Hog Heaven Saloon, where they meet the foul, morbidly obese mob boss, Krew, and his bodyguard Sig. Jak and Daxter work for Krew for a time, in exchange for upgrades to the Morph Gun.

Krew reveals that Baron Praxis is working with the Metal Heads to keep the people distracted from his own corrupt governing. In light of this, Torn sends Jak and Daxter on a missions to find Vin, a paranoid scientist, and Ashelin Praxis, a high-ranking member of the Krimzon Guard who works with the Underground. Ashelin reveals that Baron Praxis is interested in artifacts related to the precursor hero Mar.

Krew also sends Jak to meet a racing manager down in the stadium (revealed to be Keira). She explains that she is working on a secret project, and gives Jak the JET-Board to keep him occupied. Jak is more interested in the prize for winning the race championship, a tour of the palace.

At the Underground hideout again, Torn tells Jak that the Shadow wants him to prevent the Metal Heads from reaching "The Sacred Site" outside the city walls, in order to protect an important artifact there. Jak and Daxter discover the Sacred Site is Samos' hut, now overgrown. The pair realize that they have been transported through time via the Rift Gate, and are now in the future. Then the Shadow is revealed to be a young Samos (who does not recognize the pair, because they haven't actually met yet).

Samos tells Jak that the boy they saw with Kor is important because he is heir to the throne of Mar, and only he can open the Tomb of Mar, where the Precursor Stone is hidden. The Precursor Stone is an artifact of great importance, and key to the defeat of the Metal Heads. Jak and Daxter destroy a statue of the Baron, revealing the Tomb of Mar below and its guardian, an oracle. The young boy is taken to the tomb, but the oracle states that the boy is too young to face the Trials of Manhood, and the door begins to shut. Jak and Daxter dive through as it closes. They complete the Trials Of Manhood, and enter the main room, which holds the Precursor Stone. Another oracle tells them that the Metal Heads nearly destroyed the Precursors. Baron Praxis arrives, and despite Jak's efforts, escapes with the Stone.

The two Samos' meet one another and argue.

Back at the hideout, Torn confesses that he sold the Underground out to protect Ashelin. Several members of the Underground were taken captive and Jak must rescue them. Afterwards, Jak and Daxter find the Samos they know. Upon returning to the hideout, Samos (both of them) send Jak to find the Life Seed in their old hut. The Life Seed would give young Samos all the power old Samos has. Old Samos reveals that he had been preparing the Life Seed for years prior to entering the Rift Gate. Jak escorts the young Samos, who reveal through meditations that Praxis plans to break open the Precursor Stone in an effort to destroy the Metal Heads. Samos confirms that shattering the stone would not only stop the Metal Heads, but also would destroy the entire world with it.

Keira reveals that her secret project is a nearly completed Rift Rider based on her studies of the original, though she's still missing two major components: the Time Map and Heart of Mar, the latter of which is in Krew's possession.

Jak races for Keira's team and wins, gaining entrance to the Haven Palace. Praxis, however, recognizes Jak and orders the guards after him. Jak and Daxter escape with the unintentional help of a bitter Captain Erol, who tries to run them down after losing the race. When Erol misses, he crashes into a crate of Dark Eco and dies in the explosion (presumably). At this point, Ashelin intercepts the heroes and holds Jak at gunpoint, demanding to know why he has been sabotaging Praxis in the war with the Metal Heads. He explains, but she doesn't believe him until a call to Vin, who confirms that her father's actions will destroy the world.

Ashelin confides in Jak and Daxter that Krew is building something for the Baron at a secret weapons factory. Jak and Daxter go there, and Krew reveals the piercer bomb, which has the power to destroy the Precursor Stone. Krew tries to buy Jak's silence with a weapon mod, but Jak refuses. Jak and Krew fight. When defeated, Jak acquires the Heart of Mar from him, but Krew activates the bomb in a last-ditch effort to kill the meddlers. They escaped with Ashelin, and Krew is left at the construction site and, like Erol, dies. After acquiring the Time Map from an arcade game at the saloon, Jak and Daxter discover that Metal Heads have still breached Haven City through Krew's treachery. Sig, who was sent on a mission by Krew, is met in the Underport, and explains that Metal Heads are coming in through a passage he had unknowingly open. Fighting their way out of the Underport, the three make it to the elevator, but Sig falls when a Metal-pede destroys the bridge he's standing on. Both warrior and beast plummet to the darkness below.

Jak and Daxter finally confront Praxis, along with a squad of guards at the construction site, but Kor appears and reveals himself as Metal Kor, leader of the Metal Heads. Baron Praxis proceeds with a charge, to which Kor responds with a fatal blast. After Kor leaves, Jak and Daxter come out of hiding and approach Baron Praxis, who shows them a second piercer bomb he intended to use all along. In his final moments, Baron Praxis says that Jak is the "supreme weapon". Daxter recovers the Stone, disarms the bomb, and saves the world.

The two use the Precursor Stone to attack the Metal Head Nest, and confront Kor. Kor reveals the boy as young Jak, and demands that Jak give him the Precursor Stone. After the resulting battle, Kor’s head flies off and he is defeated. The Precursor Stone is finally opened, and a hologram of a Precursor appears. Samos and Keira arrive with the now-completed Rift Rider to send the younger versions of Samos and Jak to the past, so they may prepare everything for the present.

In the end, the group is celebrating at the Saloon, which Daxter takes over and renames "the Naughty Ottsel". Sig reappears, to the excitement of all present, having survived his seemingly fatal battle with the giant Metal-pede. Samos mourns the deaths of all those who gave their lives in pursuit of peace and justice in Haven City. Finally, Sig gives Jak the Ruby Key, an artifact to bypass all security in Haven City, and says he's designated driver. Jak grins and adamantly says he is done with adventures. Samos cryptically comments that they may not be done, and may yet meet Mar.

The game ends as the camera pans to a beautiful, fireworks filled sky as the end credits begin to roll.