The war between Earth and the machines has finally ended, with the machines being declared as the winner. However, the aftermath of the conflict has not been favorable for the planet Earth, leaving it at a disadvantage. Warrius Zero, who had lost his dear family to the machines, is now a part of the Earth fleet working in collaboration with them. Together, the humans and machines aboard Zero's ship have been given the challenging assignment of capturing the notorious space outlaw, Captain Harlock. Despite Zero's unwavering efforts to fulfill this daunting task, he begins to sense a restlessness about the true intentions behind the newfound peace between the two factions.