In the distant future, humanity freely traverses space and has developed a way to transfer consciousness into mechanized robotic bodies as means to potentially obtain eternal life.

Although the process of mechanization is expensive, there are rumors that anyone who makes it to the last stop of the Galaxy Express 999, an advanced intergalactic transit system resembling a passenger train pulled by a JNR Class C62 steam locomotive, can get a machine body for free.

To get there is the goal of twelve-year-old street urchin Tetsuro Hoshino, living in the slums of Megalopolis City, where the 999 makes its stop on Earth for one day of each year.

She saves him from the police and uses a device to look into his dreams, where she watches a young Tetsuro lose his mother to the villainous Count Mecha, who hunts humans for trophies.

Awakening in the house of an elderly woman who saved him, Tetsuro learns that Titan is governed under "paradise law", essentially an anarchy where everyone can do as they please, and that Maetel was kidnapped by the Grape Valley Bandits.

Though initially telling him not to pursue her, the old woman helps Tetsuro rescue Maetel by providing him with a hat and poncho to shield him from Titan's intense sunlight as well as a gun for self-defense, all of which belonged to her son, Tochiro Ōyama.

With this, Tetsuro sets out to find Maetel and meets Antares, the leader of the Grape Valley Bandits, after saving a young girl in his care from a machine man.

They depart Pluto, and back on the train, make the acquaintance of a young waitress named Claire, who has a machine body made of crystal glass.

The space pirate reluctantly informs Tetsuro that the Time Castle will appear next near Trader's Fork, a waystation on the arid planet Heavy Melder, the train's next stop.

At Trader's Fork, which resembles an Old West frontier town, Tetsuro finds his way to a saloon where a beautiful machine woman named Ryuzu performs a song before a tearful crowd.

Tetsuro, having made a friend in the sympathetic bartender after being taunted by some of the other patrons for ordering milk, asks if the old man might know where the Time Castle will appear, sending the entire saloon into silence.

Tetsuro travels there on a ramshackle motorized bicycle and discovers a downed ship at the base of the mountain, where he encounters Tochiro living alone inside of it, with his only company being the bird Tori-san.

Tetsuro then erects a memorial to Tochiro and tries to make his way back to Trader's Fork, but gets assaulted by thugs from the saloon working for Count Mecha, who steal his gun and leave him for dead.

He discovers, much to his horror, the taxidermied remains of his mother mounted on a fireplace inside, before encountering Count Mecha, who was alerted to Tetsuro's arrival by Ryuzu, his lover.

The confrontation is briefly interrupted by a cloaked figure revealing himself to be Antares, who came to help Tetsuro fight Count Mecha in the name of his orphaned wards.

However, as Ryuzu suddenly hesitates to advance time, Antares enters to help Tetsuro, sacrificing his life when the bullets inside of him go off after being shot by Count Mecha's gun, killing him and shattering the capsule.

Before this can happen, Maetel, desperate to save her young companion, enters the room and reveals that she intends to destroy the planet with her pendant, which contains the consciousness of her father and Promethium's husband Dr. Pan (Dr. Ban in the English dub), a traitor who opposed the mechanized empire and also the mysterious voice Tetsuro heard back on Earth.

Dr. Pan explains that the pendant contains enough energy to disrupt the planet's mechanized counterparts, all of whom were transformed willingly in the hopes of someday destroying Promethium's empire.

Even though at the time the majority of theatrical anime features like Space Battleship Yamato or Science Ninja Team Gatchaman consisted of collected or expanded TV episodes, an older range of high school viewers that had been attracted to these films were increasingly displeased with these slapped-together affairs.