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 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.

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’s human! However, 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!

In this dramatic sci-fi animation, a young boy embarks on his final journey on the Galaxy Express 999, a train that travels through outer space. Along the way, he faces challenges and encounters fascinating characters, experiencing personal growth and coming of age.

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.

In a world where humans can achieve immortality by replacing their bodies with robotic ones, a young boy named Tetsuro Hoshino embarks on a journey aboard the Galaxy Express 999, a train that travels through space. His goal is to obtain a mechanical body for himself and avenge his mother's death. Along the way, he encounters various individuals with their own stories and struggles, all while exploring the vastness of outer space.