Manabu succeeded in the entrance examination of the Space Defense Force (SDF), convinces his reluctant mother to let him go and says goodbye to his homeland Tabito.He gets on Train 550 to reach planet Destiny, the headquarters of the SDF and the starting station for all of the Galaxy Express trains, and haphazardly encounters Rui who also join the SDF. All of a sudden, the train with Manabu and Rui loses its control and is sucked in a spatiotemporal warp called "the knot of time". They go back into time and arrive on planet Hakumei 5 years earlier, when Manabu met his older brother fighting space pirates...