Tetsuro's mother is murdered while the two of them travel through the snow by the villainous Count Mecha. Before she dies, Tetsuro's mother tells him to go to the planet Andromeda where he can get a machine body and not die like she did. Tetsuro passes out from the cold but is rescued by the mysterious Maetal, who gives him a pass to the Galaxy Express 999 for free under the condition that he will travel with her.

The 999 travels to Pluto, where the frozen human bodies of the machine people have been laid to rest. Tetsuro meets Shadow, the machine woman who is caretaker of the graves. Shadow shows him her frozen human body, a body so beautiful that she refused to have a face on her machine body since it couldn't compare to her human face. Shadow tries to capture Tetsuro to regain her human body, but Maetel saves him.

The 999 arrives on a planet where the entire populace except for one person have been turned to stone by a petrification cloud. The one person still alive, a warrior, attacks Tetsuro and steals his pass, hoping to use it to escape and find a cure for his lover, who was turned to stone.

Additional people arrive on the planet who seek to steal the petrified remains of the warrior's lover. Moreover an another petrification cloud is approaching the planet.

The 999 arrives on a planet where everything is encased in armor, including a panzer beetle that severely wounds Maetel. Tetsuro travels the planet, searching for a doctor who can help her. The doctor however is too old to help, and his son, who is the only other person left alive on the planet tries to kill Tetsuro.

The 999 finds its next destination destroyed; it was demolished by a planet that travels through the dimensions, smashing other planets. When the 999 lands on this planet, they are confronted by the planet's ruler, Egoterina.

Tetsuro meets Horohoro, a poor skeleton man who has lost most of his body including his ribs because he is so poor.

The 999 arrives at a planet where people are passionate and don't hide their emotions. Meanwhile a group of 4 assassins are hired by a friend of Count Mecha's to kill Tetsuro.

The 999 arrives on the planet Ulatorus, which contains mountains of screws. When a storm causes one of the mountains to collapse, Tetsuro loses his pass and meets a machine woman who kidnaps him, seeking to keep him in her home permanently. At the same time, the 999 malfunctions due to a faulty screw.

The 999 is heavily damaged and forced to land on a planet under the despotic rule of the Cowardly Elder, President Delmukade. Tetsuro, Maetal and the Conductor are forced to travel underground where they meet Delmukade, who demands that Tetsuro sell him his young body. Delmukade's son Paschal arrives, and reveals that Delmukade is the only person living on this planet; suspecting rebellion everywhere, he had killed everyone else including Paschal's mother.

The 999 approaches a large group of spherical homes, which are ruled by a Great Chieftain. Upon entering, Maetel is captured by the Chieftain's minions. Tetsuro meets Tetsuguro, a man who looks just like him and has assembled weapons to defeat the Chieftain. While they head to the Chieftain's castle however, Tetsuro is tricked by a scarecrow of Maetel and is shot.

Tetsuro is captured and brought before the Great Chieftain, who has a computer with all of Maetel's secrets. Tetsuguro manages to rescue Tetsuro, and discovers that his girlfriend has been killed by the Chieftain.

At the 999's latest stop, Deadwood Mountain, Tetsuro and Maetel meet Prider, a poor singer who seeks to board the 999 so he can become a famous singer. When Prider doesn't have enough money to board, he borrows money from his girlfriend Alice and buys a ticket on the 999. Tetsuro gets upset at Prider for abandoning his girlfriend after all she did for him. The 999 is approached by the Valkyries, a group of witches, and three of them board the train.

The three Valkyries bring everyone aboard their ship, where our heroes meet their mother, the head Valkyrie. The ship travels to the edge of the universe where the Valkyries show our heroes the bones of all the humans they've killed.

The 999 landed on a planet called "Rifle Grenade", where slaves were brought in to fight a perpetual war between two factions as spectator sport. One of the slave soldiers, Zeda, escaped and found refuge in the hotel room of Maetel and Tetsuro.

At gunpoint (from the previous episode), Tetsuro told Zeda of his struggles back on Earth. Zeda was instead moved and decided to joined the rebels. With his companions Santana and Brudas, Zeda managed to unite the two soldier factions and started to attack government facilities.

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A boy who looks just like Tetsuro, named Manabu, and his brother work hard and are able to purchase a single pass for 999. The brother passes away before they can make it to the town where 999 arrives. When Tetsuro goes out on his own, Maetel mistakes Manabu for him. Tetsuro arrives and fights Manabu, but they quickly become friends as they have so much in common. When Manabu tries to board the 999 however, he is told that the pass is counterfeit.

The 999 arrives on the Planet of the Endless Summer, which is populated by humanoid insect like creatures. The queen of the creatures captures Tetsuro and Maetel, planning to boil them to make them food for her children.

The insect babies hatch and when Tetsuro finds himself unable to kill them, they climb aboard the 999 and start eating it.