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.
The 999 takes a rest stop aboard the planet Confession, a planet said to be free of evils. Unfortunately, when a crime is discovered, the planet committee wishes to silence its witnesses.
The Battle-Torn planet is a world divided in half, between advanced and primitive beings. The primitives want Maetel to be their queen, and Tetsuro to be their sacrifice.
The 999 encounters a planet that can travel through dimensions. Its ruler, Egoterina, is mentally unstable and captures Tetsuro, Maetel and the Conductor.
On a heavily industrial world, the freedom fighter Clowmaria is trying to halt industry for the sake of conservation. As a fugitive, she seeks escape on the 999.
The 999 arrives on a world where a machine woman plates everything - including living organisms - in gold. A young boy wants this treatment to be accepted by his golden girlfriend.
The 999 arrives the Empire of the Cowardly Elder Delmukade, a ruler who assassinated everyone in the kingdom to stay ruler... and who wants Tetsuro's body.
The 999 arrives at the Visage of Memories, the Conductor's homeworld. He encounters his old lover, who has changed for the worse since he left on the 999.
