Tetsuro meets Crystal Claire, a waitress on the 999 that is made entirely of glass. Claire's body was forced upon her by her mother and she is seeking to buy back her original body. Tetsuro finds his mother alive again on the train, but it is actually a monster that tries to pull him out of the train with it.The 999 arrives on the planet Titan, where Maetal is captured by machine men.

The 999's first stop is the planet Mars, a desolate planet where few live. When Tetsuro is provided a tour by a young woman, Freme, her boyfriend Geronimo shoots Tetsuro and steals his 999 pass.

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.

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 falls into the Sargasso, where they find the remains of the 333, a missing train. Traveling aboard, Tetsuro, Maetel and the Conductor find only skeletons. A woman aboard the train, Ryuzu, reveals herself, saying that she sped up time on the train which killed everyone. Through her threats, she takes a hold of Tetsuro and departs the train's remains with him.

Tetsuro meets Clowmaria, a freedom fighter on a heavily industrialized world that is trying to get the people of her planet to change their ways.

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.

Hanako brought the still asleep Tetsuro to a neighboring planet aptly called Wildflower. They traveled to her home, and were greeted by her aging mother and ailing father. Without Tetsuro's knowledge (or consent), Hanako feigned their upcoming marriage, for which Hanako's parents were eager to prepare a banquet.

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.

On their latest planet, Tetsuro meets Freiya, a poor girl who appears beautiful to him but is considered ugly and deformed by the other inhabitants of her planet because she does not glow in the dark with a uniform light. Freiya is an amateur animator who hopes to become a director someday.

The bandit Antares sneaks aboard the 999 and starts stealing and killing people aboard. He meets Tetsuro and Maetel and forces the 999 to travel to his home by holding Tetsuro at gunpoint.

The 999 arrives at the Comet Library, where all the books published are located. There, a pair of men capture Tetsuro and try to force him into having a machine body.

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.

The 999 is attacked by the pirate ship Queen Emeraldes, which forces the train to a pirate planet. There Tetsuro and Maetel are captured by the pirate Emeraldes, a caped woman who desires Maetel's body.

Tetsuro meets Edmund, a fellow passenger on the 999 who is looking forward to returning to his homeworld on their next stop. When they arrive however the planet is completely ravaged.

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.

Hoilock's mother's dying wish is for him to continue in her footsteps in toppling those in charge of making everything gold. Meanwhile the 999 takes off without Tetsuro when he doesn't return in time.

The 999 stops at an abandoned artificial colony world. Tetsuro is pleased with its appearance but Maetel is puzzled that the colony looks quite different than it did on her last visit. They investigate further, and are set upon by a terrified mob of physically identical men. Maetel recognizes their face as being that of the colony's architect, Dr. Cyclops.

The 999 arrives on the planet Arashigaoka (lit.: Windy Hill) where a sickly father and son, Kira operate a shoe repair store. Tetsuro's pass is stolen by the father, who seeks to get on the 999 and leave the planet so he won't be a burden to Kira. Kira forces him to return it at gunpoint, who wants to obtain a pass for him legitimately.

Ryuzu brings Tetsuro to her home. There she demands Tetsuro remain with her, showing him the skeletons of those who refused her. Ryuzu offers Tetsuro a machine body, then shows him her beautiful machine body. Ryuzu tells Tetsuro her sad past, of how she was emotionally blackmailed into getting this body by her lover, but then was cruelly abandoned by him when others copied her style.

The 999 arrives at a hollow planet with no gravity; as a result everything is a lot fatter looking, and can float through the air. Tetsuro and Maetel are confronted by cattle keepers but are able to escape. As they travel to their next planet Tetsuro meets an artist who has a wooden machine body. When they travel through a planet full of leaves, an electric mushroom threatens to destroy the train.

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.

After the 999 landed on the five-planet system Snow Capital, Tetsuro and Maetel explored the city. He fell through a hidden hole which led him to the slum part of the city, and was promptly mugged by a group of local residents. Tetsuro spotted a girl, Bojin Yuki, to whom he gave his last bit of biscuit. Yuki then brought him to her home on the surface. Yuki's mother, however, wanted to cook Tetsuro for food.

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 999 is pursued by the Black Knight, a caped figure in a dark, fog drenched world. The Black Knight requests Tetsuro stay on the planet and be his friend, but Tetsuro refuses and he attacks. They then travel to the planet Yonde 3 where the son of an innkeeper, a musician, desires Tetsuro's pass so he can leave the planet.