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.
