The planet Earth has been overrun by the alien Illumidus Empire following a protracted, bloody conflict. Harlock, a captain in the Earth's fleet, intentionally destroys his ship to prevent the Illumidus from utilizing it, and he flatly refuses to join them. With the aid of his comrades Tochiro and the space pirate Emereldas, as well as his beloved Miya, he wages a terrible private battle against the Illumidus.