As Harlock has returned to the junk planet its local police force is on the edge. Meanwhile Tadashi discovers the nature of the work his dead father Daiba did on the notorious space ship.

Earth has vanished following the mysterious attack from the Fata Morgana, now a ghost ship which was once used by Professor Daiba for a scientific expedition.

Tadashi decides to accept the proposal of Captain Sherlock and to board the Arcadia.

Yattaran, Kei Yuki and the other former ship mates of Harlock are being held on the prison planet and are condemned to capital punishment. While the Arcadia strives to set them free, the commander Ilita takes the head of the space armada which should fight the Fata Morgana.

The Arcadia investigates the disappearance of the Earth. During this time, army commander Ilita prepares to engage in combat, but will they last long against the most frightening weapon of the ghost ship: fear!

The armada is decimated, and Ilita is the only survivor. While the Arcadia approaches the battlefield, Tadashi burns to revenge his father's death. But will the brave crew of the Arcadia resist the servants of evil?

On a mining planet, an evil roar resonates in the heart of a mountain. A minor has disappeared.

Maji, a former companion of Herlock, goes looking for him.

Meanwhile, the crew of the Arcadia discovers a mysterious pyramid buried in a crater of the Moon.

Yuki is brought aboard the Arcadia.

Meanwhile, Maji witnesses Tadashi being kidnapped, resulting in him being captured, too.

It is a sad fate that is reserved for them by Noo: they have no choice than to kill each other!

Come to save his friends, Herlock manages to find enough strength in himself to defeat an evil entity of Noo.

But while the crew of the Arcadia is working to unravel the mysteries of Earth by decrypting Tadashi's medallion, an insidious threat sneaks aboard the ship...

Captured by the Noo, the body of Kei Yuki surveys the corridors of the Arcadia with an aim of destroying the computer of the vessel. During this time, Kei, captive of her dreams, meets the spirits of the missing scientists, who tell her the tragic story of the crew of the Fata Morgana.

After Noo took on Herlock in a duel, the Arcadia flies to the planet Neoterra to help them in their combat against the Fata Morgana. The Noo then shows all its destructive power by causing an earthquake which shakes the entire universe. Will the Arcadia manage to escape from it?

The crew must find a way to save the Arcadia unassisted by the on-board computer.

Meanwhile, Irita engages in a fight against the Fata Morgana.

In a final act of heroism, he sacrifices himself to embed a tracker into the vessel which will allow Herlock to trace Noo...

Harlock is left alone on the ship save Mimeh. He follows the Noo into the realm the earth is hidden in. Meanwhile Tadashi is visited by his father’s ghost who tells him of a promise Harlock made him.