In a southeast Australian archipelago, Dr. Neo Cortex and his assistant, Dr. Nitrus Brio, use a device called the "Evolvo-Ray" to mutate the various animals living on the islands into beasts with superhuman strength and high intelligence in order to dominate the world. Among their experiments is Crash, a peaceful bandicoot who Cortex intends to be the leader of an army of animal soldiers. Despite Brio's warnings, Cortex subjects Crash to the untested Cortex Vortex in an attempt to control him. The Vortex rejects Crash, allowing him to escape. After Crash leaps out a window and falls to the ocean below, Cortex prepares a female bandicoot named Tawna to be used in Crash's place. Meanwhile, Crash awakens on the beach of N. Sanity Island. Having grown attached to Tawna during their time in captivity, Crash resolves to rescue her and defeat Cortex. From the beach of N. Sanity, Crash must traverse three islands until he meets his evil creator, hoping to save his fiancée. During the adventure, he will be helped by the spirit of the sorcerer Aku Aku resident on the island, who, having understood the good nature of Crash, takes his side.
The player controls Crash during his adventure. He will have to traverse the various three-dimensional levels of three islands by jumping over gaps, overcoming obstacles and collecting useful items to progress. He will also have to defeat enemies and Dr. Cortex's henchmen that he will encounter along the way, by jumping over their heads or using his special spin attack.