As resources dwindle, five hundred billion colonists return to Earth, causing the Homecoming War over Earth's remaining resources. The bloody war only ends when an authoritarian government, the Gaia Sanction, declares Earth a sacred planet forbidden to humanity. With the help of four unstoppable ships powered by alien technology, Harlock's fleet prevents Earth from recolonization until a treaty allows diplomatic elite to immigrate. Enraged by this betrayal, Harlock turns on the Gaia Sanction. With his ship, the
Arcadia, badly damaged, Harlock unleashes the ship's
dark matter. Harlock intends to encase Earth in a protective
force field, but it instead becomes uninhabitable. The
Arcadia survives but is forever changed. Now an immortal pirate, Harlock vows to atone. Gaia obscures the condition of Earth with a giant hologram to maintain power. Harlock and his crew steal 100 warheads from the Gaia Sanction to "start over". Admiral Isora recruits his younger brother, Yama, to kill Harlock. Yama agrees, desperate to atone for a childhood accident that paralyzed Isora and critically injured their mutual love, Nami. Harlock, aware of his plan, allows Yama to infiltrate his crew. During a mission to install the penultimate warhead, Yama learns that Harlock's plan is to disrupt the timestream and alter history by exploding the warheads in strategic places throughout the universe. When the mission goes awry, Yama dooms himself to save a crew mate. Harlock rescues Yama, who briefly considers executing Harlock. On board the
Arcadia, Harlock's words and attitude and the crew's acceptance convince Yama to follow Harlock. The Gaia Sanction permit Isora to use a superweapon to stop Harlock. Harlock evades the Gaia fleet using holograms. Isora destroys the
Arcadia with the superweapon, but this is another hologram. The real
Arcadia ambushes the fleet, rams Isora's flagship, and Harlock takes the crew hostage. Once at Earth and past the great illusion, the crew is horrified at Earth's fate. Isora reveals Harlock's true plan: Harlock intends to destroy the current universe and rebirth a new one. Shocked, Yama sides with Isora, and the
Arcadia moves away from Earth, apparently of its own volition. Yama helps Isora and his crew take over the
Arcadia. With the ship and crew imprisoned, Isora confronts Nami, who informed Yama of his tactical plans. Nami realizes that she is the source of Isora's torment, not Yama. Nami provokes Isora into causing her life support to fail. As Nami dies, she admits to loving him and sacrificing herself to bring him peace. Isora lies about Nami's death. Disbelieving Isora and haunted by Nami's death, Yama returns to Earth, where he finds a meadow of flowers. Yama interrupts Harlock's public execution and releases the
Arcadias crew. Yama says both he and Harlock were wrong, and he shows them a flower. Overcome by the possibility of a peaceful "starting over", Harlock abandons his previous plans and decides to expose the Gaia Sanction. The
Arcadia evades the Gaia Fleet and destroys Earth's hologram emitters. The exposed truth of Earth's condition destabilizes the Gaia Sanction, which depended on a quasi-religious veneration of Earth to legitimize their rule. Desperate to contain the situation, the Gaia Sanction's leader decides to use a doomsday
particle cannon to destroy the
Arcadia. Realizing Earth could be destroyed, too, Isora rams the
Arcadia and pushes it away from Earth. Both ships board each other, causing many casualties on both sides. Yama confronts Isora. Isora shoots at Yama's face, scarring him similarly to Harlock. Harlock mortally wounds Isora, saving Yama. When Isora warns them about the particle cannon, Harlock remarks that Isora was the only one to remain faithful to Earth. Harlock again unleashes the
Arcadias dark matter. With the
Arcadia moved further from Earth and protected by a dark matter shield, both Earth and the
Arcadia survive the cannon's blast. As Isora dies, he explains that he saved Earth because he knew Nami and their mother loved flowers. After the
Arcadia crash lands on Earth, Harlock sets the final detonator and says another Homecoming War is inevitable. Believing Earth is a gift from Nami and Isora, Yama refuses to destroy it. Liking his answer, Harlock gives the detonator to Yama and says the universe needs the myth of Captain Harlock. As the Gaia Sanction fleet confronts the
Arcadia, the crew wakes up, seemingly healed by the dark matter, and the ship escapes, now commanded by Yama who then becomes the new Captain Harlock. ==Cast==