After the last battle with Crash Bandicoot, Cortex is thrown down to Crash island and fall in a cave filled with glowing crystals. Convinced that they hold tremendous power, he takes one and gets back onto his laboratory. One year later, Cortex and his new assistant Dr. N. Gin rebuild an upgraded Cortex Vortex in outer space which will turn everyone on Earth into his mindless slaves. But they need 25 more crystals to reach the Vortex's maximum capacity, and they do not have any of their operatives left on Earth. Cortex then devises a plot to manipulate Crash into retrieving the crystals for him.