The movie version of Galaxy Express 999, released in 1979, serves as a compression of the storyline told in the manga and television series with some modifications. Maetel and Tetsuro again set out for the home planet of the Mechanized Empire, but rather than visiting over a hundred planets, as in the original manga/TV series, Tetsuro only visits four—Titan, Pluto, Heavy Melder, and Planet Maetel. Like Planet Prometheum, Planet Maetel is a mechanized world where machine bodies are made. It is implied that Planet Maetel had once been Maetel's machine body—just as the planet Great Andromeda serves as the machine body of her mother's consciousness in the sequel film, Adieu Galaxy Express 999 -- and is still somehow linked to her. Maetel says of the planet, "This planet is also me. It is half of my own heart. We're different, but both are myself."

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.