It's a sunny day in Wumpa Island and Crash is catching some rays while dozing off in a hammock. He soon has a vision projected into his marsupial brain. What first seems to be a dream is then revealed to be Aku Aku, telepathically communicating with Crash from far away. He tells Crash that he needs to wake up, because Dr. Neo Cortex is at it again, and this time he has corrupted the Tiki power of the islands to transform the native creatures into monsters.
Meanwhile, Cortex and Uka Uka hold a meeting in their evil headquarters. Cortex reveals his plan and the blueprints for a so-called Doominator Robot, which will be used to destroy Wumpa Island and get rid of the bandicoots at last. Cortex gives N. Gin, Tiny, Nina and Dingodile the job of robbing Wumpa Island of its resources to build this giant robot. Uka Uka is pleased, but he knows they will have to get rid of Crash before anything else. With Coco, Crunch and Aku Aku captured, he is the only one left out there. Giving Aku Aku a taste of his own medicine, Uka Uka locked him up with a double purpose – to prevent him from foiling their plans and to lure Crash into a trap.
Crash heads off to find Aku Aku when he is eventually confronted by Cortex himself. They engage in a fight, but Cortex loses miserably, much to Uka Uka's later dismay. When Cortex returns to his evil lair, Uka Uka reveals to him that he's been fired. His niece Nina will take his place, and she plans to use Coco's intellect to help her finish the Doominator Robot. Both Coco and Crunch are taken away as bait for Crash.
When Crash finally frees Aku Aku, he tells him all about Cortex's new mutant army. With his help, Crash can hijack these creatures' minds and control them after he beats them up. It'll be a bumpy ride, but Crash and Aku Aku will see their rescue mission through to the end.