The Galaxy Railways, which crosses the vast universe, seems to have to go out of service, as unexplainable events happen on its trains. One time, an SOS message arrives to the Galaxy Railways headquarters from Galaxy Express 999. The message was sent from the vicinity of Planet Helise, a place which is called "the planet of forgotten time", since the galactic rails end there. The elite self-defense force of Galaxy Railways, the Sirius Platoon is ordered to handle the case. While in the centre of the story are the SDF soldiers, the protagonists of Galaxy Express 999: Hoshino Tetsurou, Maetel, and the train conductor also appear.