New planets are unlocked once story objectives on previous planets have been completed. The player progresses through the story by travelling from planet to planet. Environments are presented in a somewhat linear manner, although multiple paths are available for the player. It features new weapons, such as the Pixelizer, which gives enemies an 8-bit appearance. Though Ratchet & Clank is a re-imagining of the 2002 video game, it has a variety of gameplay elements from different entries in the series, such as strafing, automatic weapon and health upgrades, manual Raritanium weapon upgrading, and the inclusion of weapons seen in later games. Clank's gameplay sections mostly revolve around solving environmental puzzles, rather than defeating enemies. Clank is not equipped with weapons instead, he utilizes punches to defeat enemies. Clank's gameplay sections are drastically different, even though the premise of navigating environments and the controls remain the same.

Clank is attached to Ratchet like a backpack, performing several functions, such as allowing diving in water, gliding through the use of propellers, and on occasion, acting as a jetpack to allow flight. As Ratchet, the player navigates diverse environments, defeating enemies with an array of different weapons and gadgets, and traversing obstacles. The main playable character is Ratchet Clank is playable in several portions of the game. Ratchet & Clank shares many gameplay similarities with the other entries in the series.

This gameplay mechanic was first featured in the original game. In Ratchet & Clank, players can use the Swingshot to grapple targets and swing across gaps.

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