In the distant future, space travel technology made it possible for the the Earth to colonize the galaxy, leading to a population explosion that exhausted resources that resulted in a severe decline in birthrate. A movement arose to return to the replenished Mother Earth, but the planet could not withstand such an epic repatriation, sparking the "Homecoming Wars." The governing body called The Gaia Communion was formed and declared the Earth an eternal sanctuary to be worshiped only from afar as humankind awaited its eventual demise on other planets. Immortal space pirate Captain Harlock has been roaming the galaxy in the ghost ship Arcadia salvaging resources from the dying planets and raiding supply ships.

Would-be botanist Logan becomes the new recruit to Harlock's band of pirates, but the skeletons in his closet are not of the same criminal league of his cohorts. He is the younger brother of Gaia Communion Prefaectus Ezra, assigned to get on board the Arcadia and assassinate Harlock before he can blow up the galaxy with the detonators he has been planing on the planets where they have landed. Before he can carry out his orders, Logan discovers that Harlock has discovered the locations of the one hundred nodes of the Genesis Clock and believes he can turn back time to a point before humanity messed things up beyond repair; however, engaging the Genesis Clock requires the destruction of everything as it exists. Logan is torn between his loyalties to his brother and Harlock's goals. As he switches sides, he learns that things are as the Gaia Communion would have the populace believe; but, in exposing the Gaia Communion's deceptions, Harlock also reveals to Logan and the crew his own true intentions.

Toei Animation's big screen adaptation of the manga series by Leiji Matsumoto - adapted a number of times before as shorts, video features, and two television series in the seventies and eighties - HARLOCK: SPACE CAPTAIN is not only a wonder of state-of-the-art animation, but also a smartly-plotted and affecting piece of science fiction for the mature viewer. While there are plenty of exciting explosions - although few aliens since the film's narrator reveals that the downside of developing the technology to move faster than the speed of light was to find out that humanity was desperately alone - the film does not lose sight of the human motivations that drive both the noble intentions and corrupt behavior of the characters (most of whom grow over the course of the story with the exception of the comically villainous Gaia Communion elites). That the film has gone straight to DVD in the United States compared to the 3D/Imax dreck that hits theater screens regularly is quite unfortunate.