Three years after being defeated by Crash Bandicoot, Doctor Neo Cortex returns to the Wumpa Islands to exact revenge on Crash and paralyzes Coco to keep her from interfering as with previous attempts. Cortex dons a Coco-inspired disguise that lures Crash to the bay where he forces Crash into battling his gigantic mech, the Mecha-Bandicoot controlled by Dr. N. Gin.
After destroying the Mecha-Bandicoot, Cortex becomes enraged and assaults Crash, throwing them down deep into the mining shafts where Cortex originally found the first Power Crystals. The two are forced to work together to escape the mine before it caves in due to large ant-like beings invading the area in search of crates filled with Wumpa Fruit. After narrowly escaping, Crash and Cortex encounter a pair of odd, anthropomorphic turquoise parrots who proclaim themselves as “The Evil Twins”, who have come to destroy the Wumpa Islands.