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.

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.

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.

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.

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.

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.

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.

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.

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.