The final hub location is Haven City, a war-torn environment which features combat between the three factions in most areas, and due to its war-torn state, is more limited than in Jak II. The second is the Wasteland, the largest location which can only easily be traversed using buggies found in Spargus, and features many missions and accesses other locations. The first is Spargus, a smaller city located by an oasis, which features few missions but many collectibles and side missions. There are three main locations, each very distinct from one another, which act as hubs. On many occasions, Jak and Daxter both participate in minigames of various kinds to progress, adding to the variety. Commonly featured are the heavily armed buggies as Jak drives around the Wasteland, while Jak can drive zoomers much like in the previous installment within Haven and ride leaper mounts within Spargus. Though Daxter does little beyond basic platforming and combat, Jak also participates in combat missions, in which the player can utilise his expanded Morph Gun arsenal, his Dark Jak form and the newly introduced Light Jak form. Jak 3 is a third person three-dimensional platformer, in which the player controls Jak, an athletically-built human, and occasionally Daxter, who share a similar core moveset carried over from previous titles. Additionally, the more primitive leaper mounts can be used to travel throughout Spargus, while Daxter is playable in small sections more often. Buggies, used to traverse the new desert wasteland setting, are now much more relied upon than zoomers, which are only used in the now war-torn Haven City. With eight more Morph Gun modifications, and the acquisition of Light Jak to complement Dark Jak, Jak 3 retains the mix of platforming, third-person shooting, and driving.

There is a notable expansion of gameplay upon Jak 3's predecessor. In exchange for letting him stay, Jak must now prove his worth, or be thrown out in the desert as if he were never found. He is eventually saved by Damas, the king of nearby Spargus. Accompanied by Daxter and Pecker, and with a beacon given to him by Ashelin, Jak searches the desert before collapsing nearly dead. Jak is banished to the Wasteland at the hands of the corrupt Count Veger, despite Ashelin's protests. The people blame Jak for the war on account of his dark powers, and his friendship with Kor and late crime lord Krew (both of who allowed the metal heads access to the city). A year after the defeat of Kor and Baron Praxis, war has erupted in Haven City as the surviving metal heads and newcomers KG Death Bots strike relentlessly at the Freedom League, a successor to the Krimzon Guard now under the command of Ashelin Praxis and Torn, governor and captain respectively. Jak 3 continues the tone and setting of its predecessor. It is the last title developed by Naughty Dog for the Jak and Daxter main series.

Official emulation support for the game on PlayStation 4 was added on December 6, and it was made available to purchase standalone or in a bundle alongside The Precursor Legacy, Jak II and Jak X: Combat Racing. It was released in November 2004 for the PlayStation 2, and later re-released in February 2012 and June 2013 for the PlayStation 3 and PlayStation Vita, respectively, as part of the trilogy remaster. and published by Sony Computer Entertainment. Jak 3 is the third installment (fourth chronologically) in the Jak and Daxter series, developed by Naughty Dog, Inc.

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