After Dodonpachi's pilot stopped Colonel Longhener's plan to destroy humanity, the surviving Donpachi Corps was sealed inside the moon for a thousand years. Now the robotic army, led by the entity Hibachi, has reawakened on the moon and is rebuilding to wipe out humanity again — starting with the moon colony of Lunapolis. The Donpachi Corps is resurrected, paired with sentient androids called Element Dolls that augment each ship's power. The outcome of the final battle differs depending on which Doll the player chose.