The game's story takes place immediately after the events of the second game.

The game's story takes place immediately after the events of the second game. The ruins of a space station called the Cortex Vortex

Super Adventure of Bandicoot 3 is a platform game in which the player controls Crash, who must travel back in time and gather 25 Crystals scattered across time before Doctor Neo do so. Much of the game takes place in the Time-Twisting, which acts as the hub area of the game. The Time-Twisting is split up into five chambers; only the first chamber is initially available. Each chamber has five buttons that open portals to different levels.

The goal in each level is to find and obtain the Crystal hidden in the area. In some levels, the Crystal will be located at the end of a level or must be earned by completing a specific challenge. Some levels contain a "Bonus Platform" that leads to a special bonus area, where the player must navigate through a separate area and collect everything in sight. As no lives are lost in the bonus areas, the bonus areas can be played through as often as the player desires until the bonus area can be cleared. After completing all five levels in a chamber, a sixth button that opens a portal to a boss level will appear. By defeating the boss, the next chamber will become available for play.

Super Adventure of Bandicoot 3 start the game with five lives. A life is lost when they are struck by an enemy attack or suffer any other type of damage. More lives can be earned by collecting 100 "Wumpa Fruits" or breaking open a special crate to collect a life. If the player runs out of lives, the game is over. However, it can be continued by selecting "Yes" at the "Continue?" screen.

Crash has the ability to jump into the air and land on an enemy character, spin in a tornado-like fashion to knock enemies off-screen, slide across the ground and perform a body slam to break certain objects. These abilities can be expanded on by defeating boss characters, often resulting in more powerful attacks or increased jumping and running prowess