An impoverished ten-year-old named Tetsuro Hoshino desperately wants an indestructible machine body, giving him the ability to live forever and have the freedom that the unmechanized don't have. While machine bodies are impossibly expensive, they are supposedly given away for free in the Andromeda galaxy, the end of the line for theGalaxy Express 999, a space train that only comes to Earth once a year.

The series begins with Tetsuro and his mother making their way to Megalopolis where they hope to get jobs to pay for passes for the 999. Along the way however, Count Mecha and a gang of "human hunters" kill Tetsuro's mother. Before she dies, she tells him to continue the journey they started, and to get a machine body to live the eternal life she couldn't. Tetsuro tries to forge on toward the city alone, but is quickly overcome by the brutal cold and wind. As he succumbs, he cries out an apology to his mother for failing to fulfill her wish, and hopes that in his next life he'll be born as a robot to begin with.

Tetsuro is surprised to awaken by the fireplace in the home of a a beautiful woman, Maetel, who is the spitting image of his dead mother. Maetel tells him she had heard the entire incident with a long-range directional microphone she had been idly scanning around the area with. Maetel offers him an unlimited use pass for the 999 if he will be her traveling companion, to which Tetsuro agrees. She provides him with a gun and directs him to the Count's residence, telling him that the Count and his henchmen will be too distracted with their revelries to defend themselves against a surprise attack. Tetsuro bursts in on them in their meeting hall and cuts them down with a spray of gunfire. With the Earth police in hot pursuit, Tetsuro and Maetel flee the planet aboard the 999.

Along the way, Tetsuro has many adventures on many different and exotic planets and meets many kinds of people, both human and alien, living and machine. Increasingly, Tetsuro realizes that a machine body won't fix all of his problems. In fact, most of the machine people^[a] he meets regret the decision to give up their humanity.

Eventually, Tetsuro and Maetel reach the Planet Prometheum, the final stop for the 999. He is shocked by the cruelty and indolence of the machine people there, and witnesses a mechanized human committing suicide, an event to which the others react with scoffs and derision. He asks the dying man why he wished to end his life, and is told that eternal life on Prometheum is utterly empty of joy or purpose. When Tetsuro mentions the name of his traveling companion the man is horrified and tells him that Maetel is in fact the daughter of Queen Prometheum, the supreme ruler of the Machine Empire, and that she is thoroughly untrustworthy. Testuro is outraged at having been kept in the dark and rushes off to confront Maetel. Maetel is at a loss for words, but a government spokeswoman inserts herself into their conversation and begins giving answers on Maetel's behalf. Tetsuro is not impressed and he storms off in a blind fury.

Tetsuro doesn't understand why he has been betrayed by Maetel, but Maetel has plans of her own, and seeks to destroy the mechanized civilization. With the help of her father, Dr. Ban (only named in the film), whose consciousness resides in a pendant she wears around her neck, Maetel destroys her mother and the planet. Afterwards, Maetel and Tetsuro return to the penultimate station on the Planet of Bats where Tetsuro tells Maetel his intention to return to Earth and lead it toward a new future.

Maetel, proud of Tetsuro for his decision to reject mechanization, tells him she has something to take care of and that he should board first. However, Tetsuro finds a letter from Maetel telling him that it was time for them to part ways. Maetel had secretly boarded the 777 (three-seven), a nearby train, with the intention of "leading another boy to his future". However, it is unclear as to whether or not this means that the Mechanization Empire still exists elsewhere, or if Maetel will lead the boy to some other "future". The series ends as the trains both depart the Planet of Bats.