The story of Raiden takes place in the year 2090, when a species of alien lifeforms known as the Crystals invaded Earth. The Crystals took control over most of Earth's military hardware to use in the invasion. In response, the world organization known as Vanquish Crystal Defense (VCD) develops the Fighting Thunder attack craft, a cutting-edge weapon based on Crystal technology. To survive against the invaders and fight back, VCD deploys Fighting Thunder as the only hope for humanity.