After the events of Dodonpachi, in which the pilot stops Colonel Schwarlitz Longhener's plan to annihilate humanity, the remains of the Donpachi Corps are sealed away in the moon, never to be heard from again. 1000 years later, the robotic army, led by Hibachi, have reawakened and are slowly rebuilding itself in order to wipe out humanity again, taking the defenseless moon colony of Lunapolis. The world quickly resurrects the Donpachi Corps, and aided by Element Dolls, sentient androids meant to increase a ship's power, are deployed on the moon to destroy Hibachi's army. Depending on the element doll the player chose at the beginning of the game, the ending will differ upon defeating Hibachi.