#1. Humiliating Departure
At the end of the 30th century, it is a time of space frontiers. The earthlings continue to expand their dreams and ambition to the faraway frontiers of the universe. The almost immortal cyborgs, called mechanized people, rule the earth. Our hero Commander Zero is living a hollow life after he lost his family and friends in the war between the normal humans and the mechanized people. One day he is ordered by the supreme commander to hunt down a notorious space pirate, Captain Harlock. Zero is shocked as Harlock was his fellow warrior and the best friend he ever had. However, he takes this mission as he hopes to find good reason and the true meaning of live in deep space. Helmatia, , a secret agent of Metanoid, disguises herself as an earthling and succeeds in getting the job from the mechanized committee of watching Zero's conduct.
#2. Tochiro
Tochiro, a space pirate and a friend of Captain Harlock, goes lunch at a restaurant in the Gunfrontier. He is trapped by Sylviana who wants to destroy Harlock for money. Then the town is blown up by a missile accidentally launched by Tochiro's test ship, Death Shadow When the hanging rope is put around his neck, Harlock comes to his rescue.
#3. Young Harlock
Tochiro is saved by Harlock and Sylviana is kicked out by the town folks. Emeraldas joins in and they talk about Zero, the cosmo-warrior. After enjoying a big party, the pirates leave the Gunfrontier for space. Sylviana follows them in her own ship.
#4. Patraiser in a Ruined City.
Zero is surprised that Helmatia looks like his late wife. The only diferrence is Helmatia is cold and unfriendly. Zero finds the planet where he hoped to see his soldiers was devastated. A strange robot, Batlyzer comes to talk to Zero. He learns that not all the machines are the objects of detestation. Batlyzer joins Zero's fleet.
#5. Emeraldas and Sarumatake
Emeraldas talks about why she travels around the universe. She wants to find out who built her ship, Queen Emraldas and why it was made. She heads for the planet Sarumatake where the mysterious life of the inhabitants startles the visitors.
#6. Grenader in the Forefront.
When Zero's fleet approaches El Alamein, it is attacked by a rain of missiles. Zero orders to fire the twin Wave Cannons. The cannons emit blue glare like Saint Elmo's fire and it silences the enemy's resistance.
When Helmatia takes a suspicious attitude, Zero has a dispute with a mercenary, Hevy Grenader. They fight and Zero loses his arm. Grenader respects Zero's courage and becomes his good friend.
#7. Helmatia of Metanoid.
In a fight with Grenader, Zero is saved by Helmatia. His lost arm is repaired mechanically. Helmatia consoles Zero who is troubled with his artificial arm. He knows there's a woman who controls time. He thinks that if he can push back time, he might be able to save his family.
#8. Galaxy Express 999 and Maetel
Zero gets on Galaxy Express 999 running on the infinite space railway. He is involved in a battle and hammers his enemies with his mechanical arm. He is pleased as he thinks he can beat Captain Harlock with this arm. Then he comes across Maetel who warns him that time is not an easy thing to juggle.
#9. Trail to the Past
Tochiro is trapped by the cunning strategy of Zero's fleet and is finally captured. The past episodes are unfolded revealing the relationships between Zero, Harlock and other people. Sylviana tries to sneak in only to be bitterly smacked.
#10. Battle of Technologia.
Using Toshiro as a hostage, Zero lures Harlock and Emeraldas to Technologia. The battle of the space ships breaks out.. Then Helmatia begins to carry out her true mission to destroy Technologia. A gigantic space fortress, Helcastle, roars in, dragging super gravity along. with it. Helmatia likes Zero but she can not stop her mission. Helcastle is protected from the attack of any usual weapons by the super gravity. The destruction of some nuclear reactors cause grave damage to the entire galaxy. Captain Harlock asks Zero to fire the Twin Wave Cannons (St. Elmo's Cannons) at it. Zero hesitates. He doesn't know what to do. Then he sees mothers and children running desperately on the ground. Finally he signals. "Fire!"
#11. Helcastle, The Gigantic Fortress.
The St. Elmo's Cannons destroy the central system of the super gravity. Helcastle detaches the central part and begins a direct attack again. Zero orders all to attack but the mechanized soldiers start a revolt. Zero tries to subdue the revolt with the help of Batlyzer and Grenader.
#12. The Shadow
Zero gets back control of his ship thanks to Grenader and Batlyzer. Just then, Batlyzer is blown away into space by an explosion. When he passes by Space Cruiser Yamata, he recovers the memory of his true purpose for a second. But, that is the end of the robot's life.
The Arcadia destroys all the guard ships and the major parts of Helcastle. Finally the space fortress is completely destroyed. However Zero has not accomplished his mission. So, Zero challenges Harlock to a duel. While the two heroes are fighting, dark smoke from the blazing Helcastle covers them. In the darkness, Zero sees the shadow of his true enemy.
Failing to destroy Technologia, the only thing for Helmatia to do now is to help Zero to defeat Harlock. She disappears into the black smoke.
#13. Farewell, Friend! Departure with Hope.
Zero meets the giant shadow who reveals the secret about time and mechanization. He doesn't like what he is told and attacks the shadow. Then, Helmedia, hypnotized by the shadow, stabs Zero in the back as she thinks he is Harlock by mistake. The shadow just looks at Zero suffering from the wound and leaves, saying it will see him again.
Several days later, Zero wakes up in a hospital room in Technologia. He reconciliates with Harlock. He knows what he should and wants to do. His battleship, HIRYU (Fire Dragon) is repaired by the great engineer, Tochiro. Helmatia decides to go along with him.
Epilogue The earth. A mother is walking with a baby in her arms in the wild countryside covered with snow. She says to the baby. " Your father was called a cosmo-warrior.
Comos-Warrior Zero..." The mother looks up in the night sky. Zero is cruising in deep space.