During the early 20th Century, some time after World War I, aerial explorer Captain Phantom F. Harlock is embarking on what is to be the magnum opus of his long career, the traversing of theOwen Stanley Mountains in New Guinea. His major obstacle is the phantom of the witch that haunts these mountains. In a last desperate attempt to cross the mountains, Harlock ditches all but ten minutes of fuel in order to gain altitude. He carries on to his fate, amidst the mocking laughter of the Owen Stanley Witch.

Near the end of World War II, Phantom F. Harlock II is an Iron Cross-wearing German fighter pilot that flies a Messerschmitt Bf 109. During a major defeat for his side, he meets Toshiro (Tochiro) Oyama, a Japanese exchange technician working in Germany. Tochiro's project is to design a new gun sight for use in fighter planes. Harlock's most treasured possession is the Revi C-12D gun sight which he calls his "eye". Both men believe the war to be wasteful and pointless and Tochiro especially hopes that the rockets being developed by Germany may one day lead to a more positive application, such as a trip to the moon. Tochiro wishes he could escape from the war and possibly go to neutral Switzerland where he might be able to fulfill his dream. Harlock offers to take him in his plane. Stowing Tochiro in the plane's fuselage, Harlock is able to fly to Switzerland, but only after surviving a fierce aerial dogfight which disables his plane and forces him to crash land just short of the Swiss border. Carrying an injured Tochiro across the river to sanctuary, Harlock departs, giving Tochiro his Revi C-12D, before crossing back into the warzone where Harlock expects to face the consequences of his actions. Although this Harlock's ultimate fate is unknown, Tochiro pledges friendship between their two bloodlines for all eternity.

At some time in the late 30th century (circa 2960s), a Solar Federation officer named Captain Harlock returns home in his battle cruiserDeathshadow to find that aliens from the Illumidus Empire have conquered Earth and enslaved humanity. However the remaining humans blame him and other warriors like him as they were not there to protect the planet when they needed it. Harlock, along with the Tokargans who are ashamed of their role in Earth's downfall, sets out to lead a resistance against the aliens and adopts the fighting strategy of ancient marauders. During the course of the struggle, Harlock meets a former Solar Federation engineer; a Japanese man who he's never met before but feels he knows. This man, Tochiro Oyama reveals his secret project, the dreams of all his ancestors. Hidden in a deep cavern under the occupation headquarters is a space battleship that he designed and built. This ship is called Arcadia, in honor of the eternal friendship forged between Phantom F. Harlock and Tochiro Oyama during another ancient war.

Harlock also meets Emeraldas, an old friend, who immediately offers herself to the cause. The Tokargans, after witnessing the death of the last female of their race, sacrifice themselves to save the Arcadia from the life sucking flames of the Flame Stream Prominence (aka the Owen Stanley Witch of Space). Harlock's lover and voice of the Underground, Maya is killed by Illumidas gunfire. After Herlock has honorably defeated the occupational commander in ship-to-ship combat, the quisling ruler of Earth, Triter, nonetheless declares Harlock and Emeraldas outlaws and exiles them to space. Amidst an Earth that prefers servitude to their new masters over the hard but noble fight for freedom, Harlock, Emeraldas, Tochiro, and their new pirate crew of idealists and romantics set for the stars, heading out for parts unknown.