Arcadia of My Youth (Waga Seishun no Arcadia) reveals the past of the celebrated trio Captain Phantom F. Harlock, technological wizard Tochiro, and the free trader Emeraldas. Harlock is not a pirate, but a rebel defying the Illumidus Occupation Force and those who aid their occupation of Earth: his skull and crossbones banner symbolizes his dedication to fight to the death for his beliefs. Harlock's efforts to aid the people of the planet Tokarga, whom the Illumidas have used and plan to discard, becomes a baroque sword-and-spaceship epic in which heroic men weep, women display steely courage, and everyone follows a bushido-based code of honor. During the adventure, viewers discover how Harlock lost his right eye and Emeraldas acquired the trademark scar across her face.

Harlock is an early aviator, exploring the world in the skies, constantly challenging himself, and conquering the unknown as well as his own fears. A proud man, who finds himself attempting to conquer the Owen Stanley Mountain range in New Britain, which had never been done before. He finds his biplane unable to climb high enough, and has to turn back in defeat. As he turns away, he imagines the spirit of the mountain laughing at him! Unable to accept defeat, he jettisons all of his fuel except for 10 minute's reserve, and turns back to conquer the mountain. He realizes it will most likely be a one way trip, with him crashing after he clears the summit, but is undeterred, focused on his dream and his goal. He succeeds, only by sacrificing everything.

The movie makes a HUGE turn then, fast forwarding to the present circa 2277. Harlock's descendant, Captain Harlock, is the greatest and best in Earth's space fleet. Much like his ancestor, a proud man who would risk all for the right cause. Earth has been fighting against an alien race of conquerors, the Illumidas, who are very much like ourselves (human, with light green skin and different hair patterns). They conquer one world after another, pressing the conquered into service, and harvesting all the resources available from the conquered world, however they have the habit of destroying conquered worlds once the resources have been tapped. Earth fought bravely against a much larger and more advanced foe, and has lost. Earth has been conquered by the Illumidas, who are pillaging the planet for all of its resources. Earthmen serve under the Illumidas, as workers, servants, and militia-fighting fellow Earthmen who rebel against the Aliens. Harlock attempted to save a bunch of Earth's refugees in his space battleship, the Deathshadow, and find a new world where man could live free. He is returning to Earth in defeat. The Illumidas foe is too great, and there are no places where we can go without running into the Illumidas. Harlock has given his all, and fought valiantly, but to no avail, only delaying the inevitable. He now returns with the refugees, to surrender his ship to the Illumidas, so the refugees can come home to Earth safely. Once he has landed, the enemy offers him a job in their service, he will never fly again otherwise, and they were impressed with his bravery against them. An offer that is refused, as he would rather serve no one than to serve the enemy. He faces unemployment, uncertainty, and eventual starvation, as Earth's resources are running out. Things seem to be as bad as they can get. His family is gone, and his woman is being hunted down, as she is the head of Earth's resistance movement.

Just when it seems things can't get worse, he meets a small man named Tochiro, who at first seems to be a beggar, but in reality was the best Engineer in Earth's fleet before Earth's surrender. He has secretly built a ship. He has been waiting for the right person to captain it. He and Harlock become fast friends, discovering that their families have crossed many times in the past, with their ancestors meeting and becoming lifelong friends throughout history, usually during conflict. History repeats itself, with Harlock and Tochiro becoming inseparable, and rebelling together against the Illumidas, using Tochiro's ship, the Arcadia. The downside is they get exiled from Earth in the process, for disobeying Earth's current government, Harlock's woman is captured and is to be executed, along with one of Harlock's few remaining friends, Emeraldas, a free space trader (and sometimes pirate). At the same time, the Illumidas decide to destroy his other friend's planet, where his friend's family is waiting for him to rescue them from the Illumidas. Harlock must choose, save the people he promised to, or save his woman and other friend, who will be surely executed if he doesn't intercede. At the same time, the Illumidas fleet seeks his head!

This film is different than most, telling how Harlock became who he is, and why he is the way he is. It ties together with the other Captain Harlock movies and TV shows, the Galaxy Express 999 TV and movies, Maetel Legend and the Queen Emeraldas ones. It also ties into the Space Cruiser Yamato Manga. The animation is high quality, and technically very accurate in its rendering of mechanics. The story is riveting, and not very happy, but realistic in its portrayal of how life can be. It has an inner story to teach the audience, a moral.