



Tetsuro's mother is murdered while the two of them travel through the snow by the villainous Count Mecha. Before she dies, Tetsuro's mother tells him to go to the planet Andromeda where he can get a machine body and not die like she did. Tetsuro passes out from the cold but is rescued by the mysterious Maetal, who gives him a pass to the Galaxy Express 999 for free under the condition that he will travel with her.

The 999's first stop is the planet Mars, a desolate planet where few live. When Tetsuro is provided a tour by a young woman, Freme, her boyfriend Geronimo shoots Tetsuro and steals his 999 pass.

Tetsuro meets Crystal Claire, a waitress on the 999 that is made entirely of glass. Claire's body was forced upon her by her mother and she is seeking to buy back her original body. Tetsuro finds his mother alive again on the train, but it is actually a monster that tries to pull him out of the train with it.The 999 arrives on the planet Titan, where Maetal is captured by machine men.

The bandit Antares sneaks aboard the 999 and starts stealing and killing people aboard. He meets Tetsuro and Maetel and forces the 999 to travel to his home by holding Tetsuro at gunpoint.

The 999 travels to Pluto, where the frozen human bodies of the machine people have been laid to rest. Tetsuro meets Shadow, the machine woman who is caretaker of the graves. Shadow shows him her frozen human body, a body so beautiful that she refused to have a face on her machine body since it couldn't compare to her human face. Shadow tries to capture Tetsuro to regain her human body, but Maetel saves him.

The 999 arrives at the Comet Library, where all the books published are located. There, a pair of men capture Tetsuro and try to force him into having a machine body.

The 999 falls into the Sargasso, where they find the remains of the 333, a missing train. Traveling aboard, Tetsuro, Maetel and the Conductor find only skeletons. A woman aboard the train, Ryuzu, reveals herself, saying that she sped up time on the train which killed everyone. Through her threats, she takes a hold of Tetsuro and departs the train's remains with him.

The 999 landed on a planet called "Rifle Grenade", where slaves were brought in to fight a perpetual war between two factions as spectator sport. One of the slave soldiers, Zeda, escaped and found refuge in the hotel room of Maetel and Tetsuro.

Tetsuro and Maetel arrive on a planet filled with kind hearted, hard working people. When a storm ends up destroying the hotel that they are staying in, their luggage, including their passes are lost.

The 999 arrives on a primitive planet populated with people who are scared of the passengers taking over the planet. Meanwhile a friendly dinosaur named Tiny befriends Tetsuro and tries to get passage on the 999.

The 999 passes the Curiosity Planet, a planet with a large red dot on it that makes the planet look like an eye. The Conductor orders the passengers to not stare at the planet, but one of the passengers, a young woman named Miiru whose boyfriend was pulled out of the train to the planet does. This enrages the planet, which sends its moons after the 999 and orders the passengers to come off. There they find Miiru's boyfriend. The planet demands that the Conductor remove his clothes, which he refuses. Tetsuro and Maetel do so instead so he doesn't have to. The planet then demands Maetel be cut open so it can see her insides. This enrages Tetsuro, who using a knife from Miiru's boyfriend cuts open the planet. Exposed, the planet is embarrassed and commits suicide after the 999 flies safely away.

The 999 stopped at the City of Flowers, which was covered with flowers. When Tetsuro and Maetel went to the Hotel, a fire broke out that ravaged the planet (and the flowers). The train made an emergency take off, while Maetel and Tetsuro were rescued by Coa and Rea (who started the fire), and their children Mia and Doa. The flowers, Coa explained, were poisonous, and those who destroyed them were executed. The police discovered Coa's role, and ordered his execution. The family refused to come out, and the ploice threatened to seal their entrance. The people rose up in defiance, however, and the police captain was forced to back down. Now on board of the 999, Maetel and Tetsuro contemplated on the significance and irrationality of Coa's (and his family's) sacrifice.

The River of Purgatory was a barren planet, and crops often grew with great difficulty. Almost all of the pioneers sent to the planet either died or left. Gombei and Yosaku, father and son, were the only two left on the planet. While Gombei kept on ploughing the field, believing that one day his hard work would prevail, Yosaku wanted to leave the planet. A giant bird flew to Gombei's field and picked Gombei's crops. Though Tetsuro managed to chase it away, it came back and started eating off Yosaku's field. Gombei tried to drive it off but was injured. Seeing this, Yosaku came to his father's defense. Tetsuro gave the fatal blow to the bird, and Yosaku, decided to remain on the planet, and worked the land until it became fertile.

Tetsuro meets the robot owner of the robot cat, Neko. Meanwhile all the robot cats on the planet stage a rebellion. Armys of robot cats fill the skies. The army tries to fight them off but is ineffective against their small size and sheer numbers. Flying Kuro, who is just a flying cat and not a robot cat is caught in the crossfire, but is rescued by the robot cat from before. The army then takes Flying Kuro hostage. Tetsuro and Neko have a disagreement over the value of life, and the cats stop rebelling. However then all the cat robots are gassed to death. Neko is arrested but then she blows up a truck and is shot to death. Flying Kuro then walks away into space and leaves the planet behind, Tetsuro and Maetel get back on the 999 and do the same.

The 999 arrives at the Battle Torn Planet, a planet that was split in two due to arguments over whether the planet should be scientifically advanced or primitive. Soon after disembarking, Tetsuro is kidnapped and Maetel is viewed as Queen by the planet's primitive occupants.

Maetel and Tetsuro remained in Yaryabol's mansion to find out what actually happened to his mother. But instead Tetsuro was lured to a trap designed to kill him but managed to (barely) escape. Maetel confronted Yaryabol but was herself restrained by Yaryabol's mother, who ordered him kill Maetel. Though initially reluctant, Yaryabol succumbed to his mother, only to be stopped by Tetsuro. Tetsuro discovered that Yaryabol's mother was a crude robot, and her consciousness was transferred to a supercomputer by Yaryabol. Tetsuro destroyed the computer in a final confrontation, and Yaryabol was devastated believing he was unable to achieve anything without his mother on his side. Meanwhile, the Conductor managed to convince C62 to reverse its course to retrieve Maetel and Tetsuro.

Tetsuro gets lost taking an elevator that takes him to the fourth dimension. Maetel rescues him and he shoots a flashy dude who turned out to be a cyborg, then they get out and happilly continue on.

The train passes through a loose zone where everyone becomes loose and lazy and otherwise irresponsible. Tetsuro gets thrown out of the train somehow and the Conductor and the train are too lazy to look for him. Maetel is virtually unaffected. Tetsuro then ends up in a giant trash heap where he is chased by a monster made of trash. Eventually Maetel rescues Tetsuro on an uninhabited garbage planet. When the 999 leaves a much larger garbage monster attacks it but then collapses.

Tetsuro meets a man who would like to be a manga artist but can't do so because the planet has a caste system. Maetel's suitcase is stolen and the passes are taken. They have the manga artist thrown in jail with an execution pending if he is found guilty. He is found innocent but they will kill him anyway. Then it turns out his sister actually stole the passes. He has a spazz attack, runs into open traffic and gets hit by a car. As he sits in bed dying he dreams he could only find the books he read as a child then he dies. His sister regretfully returns Tetsuro and Maetel's passes having killed her brother by stealing them. But they forgive her because he at least died a peaceful if not delusional death.

Tetsuro travels to a planet where humans evolved from bees and hornets, and the two of them are poised to have a war. Tetsuro tries to make peace between them but just ends up thrown in jail. Then an all out War starts. Everyone dies but a film is left behind. Tetsuro and Maetel continue on.

Ryuzu brings Tetsuro to her home. There she demands Tetsuro remain with her, showing him the skeletons of those who refused her. Ryuzu offers Tetsuro a machine body, then shows him her beautiful machine body. Ryuzu tells Tetsuro her sad past, of how she was emotionally blackmailed into getting this body by her lover, but then was cruelly abandoned by him when others copied her style.

The 999 made a stop on the planet Trader, a junction for different major rail lines. Tetsuro met a woman in destitute and decided to treat her for a meal. But this angered a mob of similarly impoverished people when he could not extend his generosity.

Hanako brought the still asleep Tetsuro to a neighboring planet aptly called Wildflower. They traveled to her home, and were greeted by her aging mother and ailing father. Without Tetsuro's knowledge (or consent), Hanako feigned their upcoming marriage, for which Hanako's parents were eager to prepare a banquet.

The 999 arrived at the formless world Naruba, where humans often traveled to end their lives. Two adolescent shape-shifting blobs kidnapped Tetsuro and Maetel and impersonated them for a chance to leave the planet.