After the events of Crash Bandicoot: The Huge Adventure, Cortex and his minions were jettisoned into deep space. N. Tropy, now working solo without Cortex, has been given the opportunity to prove himself to Uka Uka as a true evil genius. Instead of constantly fighting against his enemies, he plans to brainwash Crash, Coco, and Crunch, turning them to the side of evil. With their help, he can finish his ultimate plan: the creation of a twisted universe made in his own vision.

To achieve his mad goals, N. Tropy enlists the help of N. Trance, a dimension-jumping misfit with the power to bend time and space. N. Trance succeeds in kidnapping Coco and Crunch, but Crash manages to escape.

Now Crash must travel to N. Trance’s twisted realm, battle and rescue Coco and Crunch, and ultimately defeat N. Trance and N. Tropy... or lose his friends to the villainous duo forever.