Captain Harlock and the Queen of a Thousand Years takes place in an undisclosed point in the future (the only reference to its date being a single reference to “the eruption of Krakatoa 700 years ago,” placing its approximate date at 2583), after humankind has colonized the distant stars. But prosperity has corrupted the people of Earth, who have become corrupt and decadent.

The Mazone, a race of sentient plants, hatch a plot to seize Earth after their own planet is destroyed. A lone scientist attempts to warn the people of Earth, but at the cost of his reputation and life. The titular Harlock is blamed for the various instances of the Mazones’ attacks upon the Earth, and, despite being an outcast amongst his own people, plans to stop the Mazone and save humanity from the alien threat with aid from Princess Olivia, next in line to throne of Millennia, the Mazones’ supposed allies in the invasion.