- 1-8: Captain Harlock and Tadashi Encounter the Mysterious Mazon: A mysterious sphere crashes to Earth. After Tadashi Daiba's father is killed by alien Mazon, he is invited to join Space Pirate Captain Harlock on his ship, the Arcadia. Tadashi gets a taste of the pirate life. A Mazon stowaway gives Harlock insight into their nature.
- 9-18: Fighting the Mazon on Land, Underwater, in Space and on Venus: The Mazon set a trap for Harlock on his pirate asteroid, using the false image of an old comrade. The Arcadia discovers an undersea Mazon pyramid in the Bermuda Triangle. After engaging a Mazon fleet in space, Harlock realizes that the Mazon have infiltrated the Earth. Harlock and his crew seek out and engage the hidden Mazon on Earth. Harlock visits the Mazon base on Venus and learns of Queen Lafresia.
- 19-28: The Mazon and the Enslaved Tokagans: Mazon guerilla soldiers trick their way on board the Arcadia. Tadashi's misfortune leads to an encounter with a Mazon slave captain, the Tokagan, Zoll. The Arcadia stops for repairs at Deathshadow Island, another hidden asteroid base. Afterwards, Queen Lafresia draws the Arcadia into a region of space where she can mind-probe the crew, and is puzzled by what she finds. The attack of a lone Mazon fighter allows Yuki Mori an opportunity to give Tadashi a confidence boost.
- 29-45: The Secret of the Mazon and the Tokagan Rebellion: The Arcadia becomes caught in the gravitational pull of a "reaper" planet. Later, unknown space projectiles turn out to be camouflaged Tokagan fighters, and Tadashi is captured. Harlock pursues Tadashi's Tokagan captors to an ocean planet, and discovers that the Mazon come from seeds. The enslaved Tokagans rebel and destroy the Mazon seed planet.
- 46-55: Queen Lafresia on Heavy Melder: After an unfortunate incident with two surprisingly human-like Mazon soldiers, the Arcadia visits planet Heavy Melder to honor the grave of Tochiro, Harlock's old friend (and builder of the Arcadia). Queen Lafresia has a parley with Harlock on Heavy Melder and shows an honorable side to herself.
Below is chapter by chapter breakdown of events.
Volume I
(Chapters 1-16, and a 17th Bonus chapter)
- A giant black sphere crashes to Earth. Professor Daiba tries to warn the Earth President but is dismissed, and then later killed by a mysterious woman in black. The mysterious Captain Harlock saves Daiba's son Tadashi from the mystery woman. Tadashi agrees to meet Harlock's crew at an abandoned spaceport.
- In space, the battleship Arcadia raids an Earth cargo vessel. On Earth, the President arrests Tadashi Daiba as one of Harlock's collaborators. Arcadia's First Mate Yattaran and crewmember Kei Yuki break him out of prison. Mazon fighters attack their escape ship but Tadashi, Yattaran and Kei safely make it back to the Arcadia.
- Tadashi meets members of the Arcadia's crew. A Mazon robot ship attacks but the Arcadia easily destroys it with its main guns. Harlock gives Tadashi a pendant with which Tadashi may signal the Arcadia at any time. Back on Earth, the President brings Tadashi to a government briefing given by the eminent archeologist, Dr. Cuzco.
- Dr. Cuzco identifies the writing on the crashed alien sphere as ancient Earth hieroglyphics. The Earth government ignores his warnings of an invasion. A Mazon agent subsequently kills Dr. Cuzco. Tadashi triggers the Arcadia signal pendant and joins Harlock's pirate crew.
- Tadashi boards the Arcadia and pledges himself to Harlock's cause. As he wanders around the ship he is surprised by the lax and absurd characters he encounters. He runs into a stowaway, the President's mysterious secretary.
- Tadashi is disturbed by the laziness of the crew. However, when a Mazon ship attacks, he sees how capable the crew can be. A captured Mazon warrior threatens Harlock with the name "Queen Lafresia" and self-destructs. Tadashi smuggles food to the girl stowaway who he has been hiding in his cabin.
- A gaseous sphere lands on Earth and the Arcadia investigates. The stowaway secretary reveals that she is Mazon, and that the environment inside the gas sphere is the same as that of the Mazon's home planet. She sacrifices herself by ripping open the gas enclosure, proving to Harlock that she has "heart".
- Harlock and Mimay reminisce about their first meeting. Harlock and Daiba go on patrol in Spacewolf fighters and retrieve wreckage from a Mazon patrol ship. Early human markings are discovered on it. They puzzle over the similarities between human and Mazon culture.
- The Arcadia sights space pirate Emeraldas' ship, the Queen Emeraldas. Moved, Harlock decides to visit the Pirate Island Asteroid. Inside, he finds Emeraldas, who uncharacteristically tries to seduce him. Harlock destroys the false phantasm as well as the Pirate Island Asteroid, knowing that his memories are safest in his own heart.
- An image of the Earth appears "skewed in half" on the Arcadia's surface monitors. The ship tracks a signal source below the waves and, after dropping a depth charge, discover a Mazon pyramid on the ocean floor. The Arcadia is pulled down towards the mysterious structure.
- The bow of the Arcadia embeds itself in the face of the pyramid . Venturing inside, Harlock discovers a sleeping Mazon, whose signals the crashed black sphere apparently homed in on. Returning to space, Harlock decides to follow the transmission back to its source in order to take the attack to the Mazon.
- Harlock misses his old friend, who had originally built the Arcadia. An Earth ship appears but flies away in cowardice. The projection of a mysterious Mazon woman is projected into Harlock's cabin and it delivers a warning from Queen Lafresia. Mimay realizes it is being transmitted from a nearby ship and the Arcadia destroys it. A Mazon fleet heads towards the Arcadia.
- Harlock defeats the Mazon fleet with 3-dimensional space tactics. He boards a surviving ship and finds a sleeping Mazon controlling it as a central brain. Dr. Zero determines that the Mazon is a plant life form. The Mazon fleet destroy their damaged ship, and Harlock decides to return to Earth to determine how many Mazon have infiltrated the planet.
- Harlock's crew find and kill various Mazon on Earth disguised as humans. Mimay tries to address Daiba's misgivings about killing beautiful creatures. Tracing the Mazon to South America, Harlock and Daiba enter the Amazon jungle and are surrounded by a forest of reanimated Mazon.
- A snow-generating device from the Arcadia causes hibernation in the Mazon forest horde, allowing Harlock & Daiba to escape. Later, they examine a strange piece of pottery picked up by Arcadia engineer Maja on a museum looting, and determine that it has a Mazon warning written inside. While drifting on the sea, torpedoes are fired on the Arcadia.
- The torpedoes are found to belong to a WWII submarine. Harlock moves to investigate but is instead distracted by a Mazon mothership in space. The mothership is destroyed, and through a captive Mazon Harlock learns that the Mazon base is on Venus.
- Space Battleship Deathshadow (Bonus story from Tale of A Time Gone By No.11, 1975): The space pirate Harlock protects a red planet from space invaders. On the planet are only male survivors. He destroys an invading fleet, which is helmed entirely by females. The women descend to the planet, ensuring the survival of the human race. Harlock remains on the Arcadia and flies off into space alone.
Volume II
(Chapters 17-34, and a Bonus chapter)
- Landing on Venus, Harlock discovers the remains of an ancient, ruined Mazon base inside a desiccated, carbonized forest crater. A robot appears but is quickly dispatched. The image of Queen Lafresia suddenly appears...
- Queen Lafresia's image gives a warning to Harlock and departs. Harlock is disgusted with the lack of societal progress on Earth, but Mimay reminds him of his old friend's dedication to humanity and he is re-invested.
- Tadashi remarks that the Arcadia seems to behave like a living being. Mazon soldiers appear, but Mimay says they are just shadow images. A small Mazon troop ship attaches to the underside of the Arcadia.
- Unfortunately some of the Mazon shadows turn out to be real intruders and the Arcadia crew engage them in battle. Tadashi discovers and enters the small Mazon troop craft and is trapped inside when it escapes. Harlock tracks down the Mazon mothership and destroys it. The troop ship carrying Tadashi is damaged in the blast.
- Mimay boards the troop ship and meets its pilot, a Tokagan slave soldier of the Mazon named Zoll. After befriending the crew of the Arcadia, he provides information about the Mazon fleet. Finally, he commits suicide for his shame at being a Mazon slave for so long.
- Before heading out towards the Mazon fleet, the Arcadia makes a rest and refueling stop at Deathshadow Island, another asteroid base. While swimming, Mimay is attacked by a giant crab.
- After having the crab for lunch, the crew examine Zoll's information capsule regarding the Mazon fleet. They depart Deathshadow Island, determined to face the dangers ahead.
- Another Mazon sphere lands on Mars, confirming Earth's position for the approaching Mazon fleet. The Arcadia pursues the homing signal and encounters a large black shape in space.
- Inside the black cloud, the crew of the Arcadia are mind-probed by Queen Lafresia. Harlock consults the ship's computer alone.
- Queen Lafresia is puzzled by the results obtained from the mind-probe of the ship's computer, which is seemingly a living member of the crew.
- Mazon agent Jorjibel's fighter engages with the Arcadia under Queen Lafresia's orders. Yuki and Tadashi launch to engage her.
- Tadashi saves Yuki from Jorjibel's attack. When Jorjibel confronts Yuki aboard the Arcadia, she reveals that she is aware that Yuki let Tadashi save her on purpose in order to give the new crewmember a morale boost. Harlock releases Jorjibel after she refuses to give any information about her forces.
- Jorjibel reports her findings to Queen Lafresia. The Arcadia is caught by the gravitational pull of a strange planet.
- The Arcadia is unable to escape from the "reaper" planet's pull and is drawn down to its surface. While Harlock's ship is immobilized, Queen Lafresia chooses that time to fire on it.
- The Mazon's attacks strangely miss the trapped Arcadia. The Arcadia suddenly regains mobility again and escapes the reaper planet, just before it explodes. A debris meteor approaches the Arcadia on a collision course, but an unknown force disintegrates it before impact.
- Harlock consults with the main computer to discuss the recent mysterious phenomenon. A Mazon ship comes into view and Harlock destroys it, annoyed that Queen Lafresia is toying with them.
- Queen Lafresia and Harlock both ponder the strange unknown forces interfering in their conflict.
- While Harlock analyzes some recent space activity on the time radar, Tadashi enhances the Arcadia's main guns with some modifications. When projectiles approach, Harlock orders the ship's enhanced main guns to fire on them.
- Great Pirate Harlock (Bonus, from Sexaroid No.4, 1970): Space Pirate Harlock helps an Earth soldier named Sado get revenge on his cheating wife and comrade. Harlock later sacrifices his own life to destroy the Earth fleet, after giving Sado control of the Deathshadow. Sado becomes the new Captain Harlock.
Volume III
(Chapters 35-55, and a Bonus chapter)
- The Arcadia is rocked by explosions caused by the projectile attack. More projectiles appear and begin to strangely home in on them.
- Tadaiba launches in a Spacewolf to investigate the seemingly-directed objects. They turn out to be Tokagan ships, and they surround Tadashi's fighter.
- Pursuing the Tokagan ships holding Tadashi hostage, the Arcadia endures a punishing trip through an asteroid ring and find a sea planet. Mazon ships appear and engage the Arcadia.
- The Arcadia dives into the sea to evade the Mazon forces. It's main guns destroy the Mazon bomber ships in the sky. The crew discovers a field of underwater pyramids.
- Queen Lafresia decides to allow the Arcadia to proceed deeper, in order to observe the crew's reactions when they discover the Mazon's true nature. An opening appears on the largest pyramid.
- Inside the pyramid they encounter nut-like capsules, which are apparently Mazon seeds.
- Harlock's crew rescues Tadashi from his crashed ship among the bed of seeds. As the Arcadia departs from the surface of the ocean planet, Mazon ships move to intercept, but Queen Lafresia receives reports that the Tokagan's are staging a rebellion against the pyramids.
- The Mazon bombers abandon the planet and the Arcadia's main computer senses that the Arcadia needs to similarly escape. The Tokagan's attack on the pyramids causes the Mazon seed planet to explode.
- A lone Tokagan ship survives the detonation and proceeds to pursue the Mazon bombers. The explosion debris catches up to the Arcadia, forcing it to evade the shock-waves.
- The Arcadia saves the Tokagan ship from a giant debris fragment from the exploding Mazon planet. The Tokagan survivors learn of their father Zoll's regret.
- The Arcadia's crew wonder if humanity came from Mazon seeds. The Tokagans depart to go their own way.
- Harlock considers the Mazon's origins and their link with mankind. He orders another rest stop at Deathshadow Island, the pirate asteroid base.
- The crew relax on the asteroid's artificial underground sea. Two Mazon unwittingly land on the surface of the camouflaged pirate base to play a game, but are alerted to the asteroid's true nature when Yattaran inadvertently causes an explosion.
- When the two Mazon soldiers begin to explore the island's interior, Yattaran is reluctantly forced to kill them in order to maintain the security of the island.
- The Arcadia decides to detour to planet Heavy Melder to honor an old friend (who also originally built the Arcadia), as Queen Lafresia observes with curiosity.
- On Earth, strange plant life phenomena increase. The President decides to escape to Heavy Melder.
- The Arcadia approaches Heavy Melder, site of his great friend Tochiro's grave site. Upon hearing of Harlock's approach, the populace panic (except for the tavern barkeep).
- Harlock honors Tochiro's grave as the crew enjoy themselves at the tavern. Queen Lafresia suddenly appears.
- While Queen Lafresia declares a cease-fire parley, a Mazon fleet appears above Heavy Melder. The Arcadia takes off on its own volition as the Mazon ships fire on it.
- The Arcadia's computer brain destroys the Mazon ships. Queen Lafresia returns to her ship and apparently executes the impulsive commander.
- As the Arcadia departs Heavy Melder, Harlock has capsules fired into the atmosphere which produce wine-flavored rain as a salute to Tochiro.
- Queen Emeraldas (Bonus, Shonen Magazine 1978): The two space warships the Death Harlock and the Queen Emeraldas attack each other in order for their respective captains to gain access to each other's half of a treasure map. Later, Emeraldas' ship is attacked by an armada and the Death Harlock goes to her rescue. When the Death Harlock continues towards another fleet protecting the treasure, the Queen Emeraldas moves to return the favor.