Somewhere southeast of Australia rest three little islands, teeming with wildlife. Two humans, however, have been experimenting with the local furry creatures in order to form a destructive and evil army of mutants. Doctor Nitrus Brio creates a machine called the Evolvo-Ray, an invention capable of turning animals anthropomorphic, but his ever pushy employer (and main series antagonist) takes the credit. One night in his castle, Doctor Neo Cortex has just captured two bandicoots; one male and one female. They are both put under the Evolvo-Ray and both work successfully. Dr. Cortex plans to make the male the leader of his Cortex Commandos for world domination and inserts the evolved male (Crash) into his patented Cortex Vortex, a mind-controlling device designed to brainwash mammals and turn them into evil henchmen, even though Dr. Brio warns Cortex that the Vortex is not ready. Crash turns out to be an utter failure and is rejected by the Vortex. He is then chased by Cortex throughout the lab, who is attempting to catch him, but the marsupial accidentally breaks through a window and falls into the sea, but Tawna (the female bandicoot and his girlfriend) is still in Cortex's clutches. Crash washes up on the beach of his home island, having survived the fall, and sets out to save Tawna before Cortex can do anything terrible to her.

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