The long war between Earth and the machine men has finally ended, ushering in a peace that is more a triumph for the machine men than for Earth. Warrius Zero lost his family during that war, yet he remains a member of Earth's fleet, which now collaborates with the machine men. His ship, composed of both humans and machine men, is tasked with the seemingly impossible mission of capturing the space pirate Captain Harlock. As Zero struggles to complete this mission, clues begin to emerge that the peace between machine men and Earth may not be as it seems.