2977 A.D. Mankind has developed the technology to head into space. They've created robots to cultivate foodstuffs on other planets and live in an age of unprecedented gluttony. Mankind receives all its food from the government and is kept in check by the government's use of hypnotic signals emitted from the television. Even high-ranking government officials have tossed their duties to the road and live a life of horse-racing and other indulgences. Captain Harlock, a space pirate known throughout Earth, is the only man who sees the impending crisis approaching. The only men who heed Harlock's words are the members of his crew on the space ship Arcadia.

The town is sent into panic by a sphere that landed. A man, who inspects the orb along with Dr. Daiba and his son Tadashi, named Professor Kusko suspects that the writing on the "Pennant" is laying claim to Earth. However, the Prime Minister continues to ignore their warnings. Then, the leader of the invading Mazone orders a subordinate to kill anyone who realizes the meaning of the pennant.

After being invited to be a pirate by Harlock, Tadashi exits the Arcadia. At the same time, Professor Kusko deciphers the characters written on the pennant and informs the people in the Prime Minister's cabinet that the Mazone plan to make Earth their second homeland. However, the government men do not show even the slightest bit of interest in the news.

A transport ship unit is attacked by an unidentified flying object as it exits Planet No.7. Believing Harlock is behind this attack, they decide to use Mayu, a girl entrusted to Harlock by his dear friend, to lure him out. Harlock and his crew experience the first aggressive attack by a mysterious enemy known as the Mazone. Realizing they are under attack, Dr. Daiba and his son, Tadashi, go to the Prime Minister's residence to plead with the Prime Minster.

Harlock tells Tadashi, upon joining his crew, to "just loiter around and enjoy it," leaving Tadashi confused. Also seeing all the crewmen merely doing as they fit and slacking off goes completely against the image he had of the Arcadia. Being stuck in such a confined space causes some mental effects on Tadashi. In that state, he sees visions of his mother who died on Neptune's satellite, Triton.

The Mazone soldier mentioned the name Queen Lafresia. Sensing the need to gather more information and wanting to test Tadashi's skills, Harlock sends the crew out to gather pieces of the wreckage from the attacked Mazone battleship. From the analysis of the wreckage, they see the Mazone may have had interactions with ancient Earth. Taking a moment's respite, Harlock sends a letter to Mayu, who is under federal governmental care.

Upon seeing an odd looking formation from space, Harlock's crew heads to the Bermuda area. Upon investigating a pyramid built by the Mazone on the ocean floor, they learn that the Mazone are actually a form of plant life. Learning that the Mazone are hidden across the globe and that the government has not heeded their warnings, the crew sets off on a search and destroy mission. Learning that there are the Mazone near Mayu as well, they set out to kill them.

There are signals being emitted from the pennant and the pyramid. These are homing signals to guide the Mazone to Earth. Sensing the direct confrontation and feeling his duty to protect Mayu, the daughter of his best friend, Harlock heads back to Earth. As they then set off for outer space, a high-ranking official is captured and gives a warning. When Harlock lets her go, Tadashi sets out after her in a fit of vengeful rage. But when his ship is hit, he begins to ...

Dr. Zero analyzes the hair from the captured Mazone and sees their make-up is identical to sap found in plant life surrounding ancient ruins. Feeling the need to investigate this association, Harlock sends out Tadashi and First mate Yattaran to retrieve the Flame Vessel.

Believing that all the jungles of Earth are inhabited by the Mazone, Harlock decides to return to the Pirate Island again. There, after a subordinate of hers was killed in South America, Alergias wages an attack on Harlock.

The Arcadia successfully makes its way to Venus. Along the way, they capture a Mazone pilot from a wrecked ship, Lola. Instead of detonating herself like the others, she just gives an ominous smile. Harlock orders Tadashi to keep an eye on her. Taking one glance at her, Tadashi becomes bloodlust and wants to kill her. However, shy hypnotizes Tadashi with visions of his late mother. Asides for foolishly divulging information on the Arcadia to her, he lets her ...

Tadashi is upset at himself for talking about the Arcadia to Lola. Then he begins practicing like mad so he can shoot in time next battle. Examining Venus, they spot formations on a fossilized continent that look like Nazca drawings. They follow it onwards to the base and find drawings about Earth from over 180,000,000 years ago.

The Arcadia heads back to Earth to investigate a third signal being emitted from the Sargasso Sea. There, the witch Aman, who was waiting for the Arcadia, wages an attack using a 1945 Imperial Japanese naval ship. Harlock, curious as to how this phenomenon occurred, sets off to investigate at the bottom of the sea

Commander Kiruta takes Mayu with him. Desperate to find her, Harlock receives a message from Commander Kiruta. "Fly to Cairo, Egypt.", "Board a Cessna.", "The Arcadia is to wait in the Valley of the Dead.

An aurora borealis of clear artificial origin disturbs the communications and electromagnetic systems of Arcadia, at the North Pole a strange being that carries out Rafflesia's commands manages to get Arcadia stuck in the middle of the eternal ice: Kirita tries to take advantage of the situation but his bombing only helps Harlock's spaceship free itself.

The operator, Kei Yuki, goes to visit her parents' grave. There, her father's ex-pupil, Kazuya, shows up. They had attempted to make a space colony not out of machines, but with nature exactly akin to Earth's. However, the experiment failed and Kazuya, the lone survivor, returned to blame her father.

Upon finding a message in a bottle floating in space that contains an SOS message from Captain Yamanaka of the Braves ship, the Arcadia sets off for the Horsehead Nebula.

he operator, Kei Yuki, goes to visit her parents' grave. There, her father's ex-pupil, Kazuya, shows up. They had attempted to make a space colony not out of machines, but with nature exactly akin to Earth's. However, the experiment failed and Kazuya, the lone survivor, returned to blame her father who had lost his life there. But now he regrets this and wants to continue the research

There are supposed to be forty-two crewman aboard the Arcadia. Searching their true colors, they try to read the minds of all at the Horsehead Nebula. After reading them all, they decide to take the next measures.

Miime's old planet is named Jura, and it was once devastated by a nuclear attack. Making one of her occasional visits to her hometown, Miime and Harlock are once again ensnared in a Mazone trap.

Arcadia, having returned to the interior of the solar system, is now located near Jupiter (astronomy); strange beings, who however immediately reveal themselves not to be Mazonians, attack her. Tadashi manages to capture alive Captain Goram (Zoru), belonging to the army of Tobaga, a small planet located in the main asteroid belt orbiting between Jupiter and Mars (planet).

Harlock is studying the precious news left to him by Goram regarding the composition of the Mazonian fleet. Rafflesia has caused a pennant to fall onto the surface of Mars coming from the Andromeda Nebula: Arcadia sets off to meet the enemy.

A little leak will sink a great ship."Upon victory, Harlock orders First mate Yattaran to secure the hostages. But, Yattaran ends up being the one who is captured! Dr. Zero, who has known Yattaran since elementary school, proceeds to tell the crew about his rarely seen genius and ability to analyze the structure of the Arcadia. The Mazone, Elza, sent on an intelligence gather mission, decides to use Yattaran's love of models to get information on the structure of the Arcadia by challenging him to a model building contest. He is to build a scale-model of the Arcadia. But, right when he completes it, Harlock and the crew show up and Yattaran is recaptured.

Zol issued the attack order! Your father!"A surprising couple, Zorba, the son of the warrior Zol, and a Mazone medic named Lucia, escaped from the Mazone fleet. There are members in the crew who doubt Lucia and think she may be a spy, but when they see that the Mazone are truly trying to recovery the two, they begin to trust her. Then the Mazone launch their general attack. Zorba is upset over his mother's execution, but Harlock yells at him and he become brave again. He decides to use himself as a decoy to protect the Arcadia. The two of them are hit by the Mazone and they sparkle off almost like a shooting star.

This is a gamble. But it's a gamble we will win."Doctor Zero becomes extremely resentful over Zorba and Lucia's murder. So, he sets off to do battle in the midst of a magnetic storm and leaves his pet cat to the ship's cook, Masu-san. He leaves alone in a fighter. Then, with the cat who snuck into the cockpit when he wasn't looking, he prepares for death in a violent dogfight. Shortly after, Tadashi informs Harlock that the Mazone mothership he shot down was actually a passenger ship. The Mazone are not just plotting an invasion but are on a mass exodus in search of a new home!