The story is set three years after the events of Crash Bandicoot: The Wrath of Cortex, where the villainous Doctor Neo Cortex and the mighty Uka Uka were left stranded in the Antarctic sea. In this game's story, N. Sanity Island comes under threat by a sinister duo called The Evil Twins, forcing Crash Bandicoot to reluctantly team up with his arch nemesis and creator, Doctor Neo Cortex, whom the twins seek revenge against.