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.