In 2977 A.C., a mysterious huge pennant is shot onto the earth from dark, unknown space. An invasion by the spaceman (Mazonese) has already started. But, earth people have not yet noticed the crises and are indulging in idle, peaceful lives. Only two persons noticed the real enemy. One of them is Dr. Daiba, a famous scientist, and the other is Captain Harlock, a great pirate traveling all over space. Harlock is feared as a pirate, but as a matter of fact, he is an indomitable youth who loves freedom and adventure most of all and never gives up his hopes even in the most difficult situations.

Dr. Daiba is killed, and Harlock decides to defend the earth and begins fighting the battle by himself.

But Tadashi, the son of Dr. Daiba, believes that Harlock is the murderer of his father and he is set to the Alkadia, a pirate ship led by Harlock, with revengeful thought, but in fact as a decoy by the government of the earth who wants to control the pirates.

Thus, Tadashi is involved in the battles with Mazonese.

And through the adventures with Harlock, he gets to realize the truth, and under the influence of Harlock, he gradually grows up in spirit.