In the future, one can achieve immortality by obtaining a mechanized body. Orphaned, young Tetsuro hitches a ride on the space train Galaxy Express 999 in the hope of obtaining a cyborg body to avenge his mother's death. Along the way, he meets Maetel, who is the spitting image of his dead mother.

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 Leiji Matsumoto's epic story, all questions will be answered and all mysteries will be revealed as Tetsuro embarks on a journey which will reveal a secret so awful, even Maetel herself can hardly bear to speak of it.

Tetsuro believed he was freeing the Earth from the clutches of the Metanoid Empire’s tyranny. Yet one year after his return, Tetsuro is a prisoner of a new tyrant, and this one human! However, before worse than imprisonment can happen to the boy, Maetel and the 999 swoop into the boy’s rescue. With his freedom, gun, and trusty hat returned to him, Tetsuro reaffirms his desire to save his home. But a new darkness is rising to swallow the light, and one of its agents has him in her sights. Before the train can depart for a new destination, Tetsuro will have to face the deadly knight Helmazaria!

While travelling on the Galaxy Express with Maetel, Tetsuro befriends Claire who was forced by her mother to exchange her organic body for crystal glass. When danger threatens Tetsuro, Claire tries to help him.

A remake of episodes 12-13 of the TV series, the 999 arrives on a planet where the entire populace except for one person have been turned to stone. The one person still alive, a warrior, attacks Tetsuro and steals his pass, hoping to use it to escape and find a cure for his lover, who was turned to stone.

A remake of episode 22 of the TV series, the 999 is attacked by the pirate ship Queen Emeraldas, which forces the train to a pirate planet. There Tetsuro and Maetel are captured by the pirate Emeraldas, a caped woman who seeks to switch her body with Maetel's.

A remake of episodes 51-52 of the TV series, the 999 crashes in a large sentient blob along with another ship. The crew tries to save the ship's pilot, a blue haired woman named Artemis, before the Galaxy Railways headquarters gets ready to blow up the blob.