The game's story takes place immediately after the events of Crash Bandicoot 2: Cortex Strikes Back, in which Doctor Neo Cortex's space station is destroyed by Doctor Nitrus Brio's laser beam device. Pieces of Cortex's space station hurtle towards Earth and crash into a tropical mountain. This sets free an evil entity known as Uka Uka, the mastermind behind Doctor Cortex's previous schemes. Uka Uka confronts Doctor Cortex and calls him out for failing to retrieve the Crystals and Gems, both of which are a great source of world energy. However, since Cortex's bumbling also managed to set Uka Uka free from his prison, Uka Uka felt a very great sense of gratitude and generosity toward Cortex. Uka Uka then recruits Doctor Nefarious Tropy to join them in their latest plan. Tropy has created the Time-Twisting Machine, a time machine that allows the villains to travel through time to find the Gems and Crystals at their original points in the timeline.