Galaxy Express 999 is the name of a train which travels through space, beginning at Megalopolis Station on one end of the galaxy and terminating at Andromeda on the other. But the Galaxy Express is more than just a train, it's also a metaphor for life itself, with passengers constantly boarding, debarking, and dreaming along the way. Tetsuro Hoshino is a youth who'll give anything to board the Three-Nine, including a promise to accompany a mysterious woman named Maetel all the way to Andromeda, the planet where, she tells him, he can get a free machine body to avenge the cruel death of his mother at the hands of the villainous Count Mecha. But nothing is as easy as it sounds, and Tetsuro is about to learn the true price not only for boarding the Three-Nine and avenging his mother, but for leaving his childhood behind, falling in love, and becoming a man.

Tetsuro Hoshino was once a boy willing to give anything to board the Three-Nine, including a promise to accompany a mysterious woman named Maetel to the other side of the Galaxy, if only to fulfill a vow to avenge the cruel death of his mother at the hands of the villainess Count Mecha. Now, two years after the events of Galaxy Express 999, Earth has become a battlefield, and Tetsuro is summoned to board the Three-Nine once more. In this, the shattering full-length theatrical conclusion to creator Leiji Matsumoto's epic story, all questions will be answered and all mysteries revealed as Tetsuro embarks on a journey the destination of which is unknown even to Galaxy Express Railways locomotive C6248 itself… a journey which will reveal a secret so awful, even Maetel herself can hardly bear speak of it.

Based on the original story by Leiji Matsumoto, this new film picks up one year after the events of Adieu, Galaxy Express 999. A young boy named Tetsuro, and his motherly companion Maetel worked to rid the universe of the Mechanized Empire who had overtaken Earth. Now Tetsuro is back home on Earth, and constantly beaten by new tyrants who took over after the machines were destroyed. Right before he is executed, Maetel and the 999 zoom in and whisk him away for an all new adventure.