This synopsis contains a detailed synopsis, and therefore, spoilers for the entire movie. It is not complete yet. The active links denote sections which are done.
In the film's opening scene, Captain Harlock's Earth Defense Force ship, the Deathshadow, takes a severe pounding in battle. Earth has lost the war and is now under Illumedian occupation. As it limps back to Earth, Harlock's ship, now carrying a band of refugees, is ordered to strike its flag and land under Illumedian guidance. The Earth flag is lowered and a black flag of mourning is raised. As the Deathshadow enters earth's atmosphere, it picks up an underground resistance broadcast from the Voice of Free Arcadia. Harlock puts the broadcast on the ship's speaker system and it lifts the spirits of the forlorn refugees.
Upon landing, Harlock crash-lands the Deathshadow to render it unusable by the enemy. An Illumedian boarding party led by Zoll, a Tokargan soldier in the service of Illumedias, storms aboard the ship to accept Harlock's formal surrender. Harlock turns in his gun and is told by Zoll to report to Illumedian HQ at 10:00. It is only 8:00 and Harlock says he has to go somewhere and will be back in time.
Meanwhile, Illumedian forces have also picked up the broadcast and are closing in on its source. Harlock is looking for the source also, as the its voice is that of Maya, his beloved. Harlock fights his way past the Illumedian forces and bursts into the broadcast room, only to find it empty. A single rose remains on the table were moments ago Maya had been broadcasting.
At
exactly 10:00, Harlock appears at Illumedian HQ. There he meets Zeda, Commander
of the Illumedian Occupation Forces. Murigson, Zeda's second-in-command, tries to soften up
Harlock, but it turns out to be Harlock who does the intimidating. Triter, prime
minister of Earth's collabrationist government, then enters. He is startled
by Harlock's appearance and cowers in silence. Zeda first admonishes Triter
for not capturing the Voice of Free Arcadia, and Triter apologizes and then
leaves. Then Zeda tells Harlock that he is impressed with his service record
and is not unwilling to give Harlock a command in the service of the Illumedians.
Harlock refuses and is told by Murigson to get lost and that he will never fly
again. On the way out he is issued a ration card by La Mime, Zeda's secretary.
The scene now shifts to a bar/restaurant. There are many Illumedian soldiers eating, drinking, and socializing with Earth women. Harlock swipes his ration card and gets a meal. He sits down at a counter and slowly eats alone in silence. Sounds of loud eating and slurping disturb him. He looks to the source and sees a stubby cloaked figure in the corner wolfing down his food. This figure is Tochiro. Harlock looks closer and notices that under his tattered and dirty cloak, the guy is wearing an Earth Defense Force uniform and like him, is also a recipient of the Badge of Combat Heroism. After finishing his meal, the figure walks over to Harlock, hands him a bottle of sake, wishes him luck, and heads for the exit. An Illumedian soldier, looking to pick a fight, trips Tochiro and taunts him. He throws a chicken leg on the ground and dares Tochiro to "get it if you can." Tochiro does, but in the course manages to make the Illumedian fall flat on his face. Angered, he moves to strike Tochiro but Harlock intervenes just in time. A mass melee breaks out and after beating up some Illumedians Harlock and Tochiro slip out in the confusion.
The pair escape to a secluded area. However, they are quickly surrounded and captured by Zoll and his troops. They are taken to some sort of research facility. Zoll probes their memories, and finds that the two have many shared memories of ages past, because at many points in the past, Tochiro's ancestors have met with Harlock's ancestors.
One
of the memories is shown. In it, it is Europe near the end of World War 2. Phantom
F. Harlock II, distant ancestor of Captain Harlock, is a Me-109 pilot in
the German Luftwaffe. After a dogfight, he buzzes a truck during landing, causing
one of the passengers in the truck, Toshiro Ooyama (Tochiro's distant ancestor)
to drop his Revi gunsight, breaking it. Ooyama is a Japanese scientist on a
technical exchange trip and had collected the gunsight for study. Harlock's
landing gear fails during landing and the plane rolls and crashes into a ditch.
Toshiro jumps out of the truck and saves Harlock just before the plane explodes.
The two men make their acquitance. Suddenly, the Allies launch an attack on
the area with tanks, artillery, and planes. Another plane is found and Harlock
prepares to take off to intercept the enemy. With no other place to go, Toshiro
hitches a ride in the back of the plane. Harlock takes off and engages the enemy.
With the help of his own beloved Revi sight, he shoots down several British
fighters but then suddenly notices that his rudder pedals are feeling mushy.
The dogfight over, Harlock flies towards neutral Switzerland where Toshiro can
take refuge. However, the plane runs out of fuel and crash lands just short
of the Swiss border. Harlock jumps out to let Toshiro out. When he opens the
hatch he sees a shocking sight. During combat, part of the rudder control wires
had been shot away. Toshiro had kept the controls working by holding the wires
together with his body, causing his hands to become severely cut. That was why
the rudder controls had become mushy. Harlock carries the injured Japanese over
the border. Meanwhile, French partisans had spotted the plane and were closing
in on the crash site. Instead of heading into Switzerland with Toshiro, Harlock
gives his beloved Revi sight to Toshiro and then re-crosses the border to face
the enemy. Here the flashback ends.
Having been found to not have any thoughts of revolting against the Illumdians, Harlock and Tochiro are set free. However, soon thereafter Triter and Zeda approach Harlock with a proposition. Harlock is asked to command an Earth ship which will be carrying a "volunteer corps" to Tokarga. When Harlock asks why Earthmen need to go to Tokarga, he is told figuratively that now he must choose between his mother and a stray dog. Harlock realizes that what Triter means is that Tokarga is to be destroyed, and he refuses. As he and Triter debate, they are interrupted by a spectacular sight. The Queen Emeraldas, damaged and trailing smoke, descends from the sky and crash lands nearby. Tochiro approaches the crippled vessel and meets Emeraldas as she emerges from the ship.
Meanwhile, La Mime visits the barracks where Zoll and his Tokargan comrades live. She has come to tell Zoll about the plans for the attack on Tokarga she overheard from the Illumdians. The news is so disturbing that La Mime bursts into tears and can only sob "Tokarga...Tokarga..."
In a ruined building, the Voice of Free Arcadia is broadcasting again. Harlock approaches the building, hoping to find his beloved Maya. But the Illumdians are also looking for the Voice of Free Arcadia. As Harlock is about to enter the building, Illumdian police units pull up. In the ensuing firefight, Harlock is shot in the eye. He sees Maya, and despite her pleas to Harlock to flee, reaches her. Then there is a laser blast, and then darkness...
Somehow, Harlock manages to stumble back to the landing site of the Queen Emeraldas, and finds Emeraldas sitting by a campfire, only to faint. He awakens to find his wounds have been bandaged by Emeraldas. During all this time, Tochiro had been busy trying to repair the damage to the Queen Emeraldas. He now emerges from the ship and declares it spaceworthy.
Emeraldas has heard the broadcast from Maya and urges Harlock to escape Earth. Harlock, realizing the depth and message of Maya's words, decides that it is the time to act. He asks Emeraldas if he could "steal" her ship so he can escape Earth. Before Emeraldas can answer, Zoll and his comrades burst onto the scene. At first, Harlock thinks they are here on behalf of the Illumedians to arrest him, but this is not the case. Zoll wants the Queen Emeraldas so he and his Tokargan comrades can return to defend their homeworld. Emeraldas agrees to let Harlock use her ship, but then it is pointed out that she would lose her Free Space Trader's certification should she loan her ship out to a outlaw. At this time, Tochiro reveals an amazing surprise: he had built a spaceship and hidden it away, and all the time was waiting for a worthy man to be her captain. Zoll demands to use the ship, but Tochiro stands fast in his determination that Harlock will be the only captain for the ship. Finally, La Mime suggests that Harlock and Tochiro go in place of Zoll, while Zoll and his men stay on Earth and feign loyalty to the Illumedians.