In a future where planets are linked by a sprawling railway network, The Galaxy Express 999 faces a crisis when it crashes on a strange planet. Among the passengers are The Conductor, Killian, Maetel, and Tetsuro, a compassionate street urchin. The SDF Sirius Platoon must now embark on a mission to save them before the Herise Time Mystery, a dangerous anomaly in the fabric of time and space, recurs.