Earth has ended a long war with an alien race of machine men, however both sides live under a stalemate-mutual truce situation. But a fuse is lit on this situation by the space pirate Captain Harlock, whose attacks on the machine men threaten to end the truce and reignite the war. Captain Warrius Zero has been appointed leader of a crew made of Earth and machine men, and is assigned the near-impossible task of capturing the legendary Harlock. However, as Zero goes about his mission, he is beset with malfunctions, mutinies, spies, and above all a secret truth that could change everything about the truce.