Space Pirate Captain Harlock

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.

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.

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.

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.

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."

The Arcadia is at the north pole after spotting an aurora that closely resembles a runway. While landing, Harlock and Miime spots a person. They encounter a Mazone soldier named Aurora, who has been waiting for over ten years to kill Harlock.

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.

A group of Mazone suddenly appear in the ship. They carelessly assume they must be holographs, but soon real Mazone appear and they begin fighting.

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.