Tetsuro Hoshino's life changes forever: his mother is murdered, and he is rescued and taken on board the Galaxy Express 999 by the mysterious woman Maetel.
The planet Pluto is a graveyard for the human bodies people sacrificed to become machine men. Its machine caretaker, Shadow, desires Tetsuro to find and retrieve her own human body.
Hanako takes Tetsuro to the planet Wildflower, where her parents reside. She tells them Tetsuro is her fiancé, soon to be married... something he doesn't know about.
The planet Nuruba is inhabited by eternal, shape-shifting formless blobs. Two of them kidnap Tetsuro and Maetel and impersonate them to get on the 999.
The 999 arrives on a planet beset by a petrification cloud, a phenomenon that turns everything living to stone. The only survivor is a warrior, who kidnaps Tetsuro to try and get on the train.
The latest planet the 999 visits is populated by people who can glow in the dark. An animator named Freiya, an outcast who cannot glow, is befriended by Tetsuro.