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.

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.