After thwarting Dr. Neo Cortex's plans for a second time, Crash Bandicoot and his sister Coco returned home for one last mission: to relax. As they were fulfilling their much-needed mission, their friend Aku Aku had a feeling something was wrong in paradise. Unfortunately, he was right...

After his defeat, Dr. Neo Cortex discovers the crystals that keep the world in balance. However, something is wrong: some of the crystals are missing. When the planets align, the chaotic flux created by the event will destroy the world. Cortex devises a plan to save the world by creating the Cortex Vortex.