
In a distant future, Tetsuro is a human boy who wants his body replaced with a robotic one. This is possible, but to do so he has to reach the Immortal Planet onboard the space train Galaxy Express 999. Maetel, a beautiful and mysterious blonde woman dressed in Russian style, joins him in the long journey through space. Every episode sees our heroes arriving in a new planet's space train station.

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'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.

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 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 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 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 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.

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 made a stop on the planet Trader, a junction for different major rail lines. Tetsuro met a woman in destitute and decided to treat her for a meal. But this angered a mob of similarly impoverished people when he could not extend his generosity.

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.
Available on: Fuji TV, Tokai Television Broadcasting, Kansai TV, Fuji News Network, Fukui TV, Hokkaido Cultural Broadcasting, Sendai Television, SAGA TV, Ishikawa TV, TNC, Television Shin Hiroshima System, TV Shizuoka, NBS, TSK, NIB, AKT, Toyama Television, Okinawa Television Broadcasting