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. 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.