Jak 3 largely focuses on the Wasteland, a large desert only briefly referred to in the previous entry in the series as being completely uninhabited and inhospitable. The game is set one year after the events of Jak II. Like its predecessors, Jak 3 takes place in an unnamed fictional universe created by Naughty Dog specially for the games. The jet-board makes a return appearance from Jak II to this game, with some additional upgrades as well. Also, the 'Dark Jak' form, introduced in Jak II, which allowed the player to transform into a more powerful offensive version of Jak, is countered by a 'Light Jak' form that mainly focuses on defensive abilities. While Jak II provided the player with only four different types of guns, Jak 3 expands on the concept with two additional modifications for each gun giving Jak a powerful loadout of twelve weapons. Spargus City, the Wasteland, and Haven City function as the main hubs in Jak 3, where leaper lizards, buggies, and zoomers respectively are the main sources of transportation. Most notably are the changes undergone in the Haven City environments.

There are some differences between Jak 3 and Jak II. In Hero Mode, Jak also keeps all twelve of his weapons but loses his light flight along with two of his dark powers until they are collected in their respective parts of the game. Collecting all 600 Precursor Orbs has some cosmetic effects on Jak's appearance, but has no effects other than this. As the Precursor Orb count is not reset, and the orbs are regenerated at their original locations, the player is able to regather orbs that they had already collected the previous time they played through the game. After the game has been completed, the Hero Mode option is made accessible, which, when purchased, allows the player to replay the game at a higher difficulty level, but with all previously unlocked cheats and extras still available. Secrets, made available as the player progresses and collects elusive Precursor orbs, can be purchased and toggled, allowing the player to access 'cheats' such as upgraded weapons damage, world mirroring, or invincibility. With the exception of timed or otherwise linear missions, the player is free to explore the massive game world as they see fit. Missions can consist of anything from defeating particular enemies, reaching a specific location, or completing a puzzle. The player is led through the story as they complete missions, assigned by the various characters in the game. Like its predecessor, the gameplay of Jak 3 is a blend of platforming, driving, and gun combat. The player uses Dark Jak, returning from Jak II, to fight enemies.

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