在这部零战士剧情/科幻/动画/战争片中,在公元30世纪的地球，努力拓展生活领域的人类，对宇宙移民满怀希望，并发展出机械化的高科技生命延续技术，同时也因为太过投入的关系，思想发生了扭曲。当时的移民者认为拥有钢铁般的身体就等于拥有永恒的生命，因而努力将自己改造成合成人（半机械人），并单方面认为原地球人会威胁他们。另一方面，地球人提倡尊重大自然的规律，反对以物理方式延续寿命，便向宇宙移民者宣战，最后因科技不如宇宙移民者而战败接受统治。在这个战乱的时空背景下，地球上出现了一位具有反抗能力的地球军舰队司令沃利尤斯·零(Warrius Zero)，他与目前在太空中四处活动且目的不明的宇宙海盗哈洛克，和想逮捕他的美丽赏金女猎人之间会发生怎样的纠葛？整个事件背后又是谁在蠢蠢欲动？
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.
