The game's story takes place immediately after the events of the second game. When the ruins of Doctor Neo Cortex's space station crash-land on Earth, they unleash an evil entity known as Uka Uka, Aku Aku's evil twin brother. He decides to join Cortex and Doctor Nefarious Tropy as they plan to gather powerful crystals that lay scattered across time and use their energy to enslave the Earth. The game follows the main characters Crash and Coco Bandicoot as they travel through time and prevent the villains from gathering the crystals by collecting them themselves.