On the road to Megalopolis, Tetsuro is encountered by Count Mecha and watches as his mother is killed. Ironically, he is rescued by a woman who looks remarkably like his mother, and they set off on a journey on the Galaxy Express 999. He begins his trek towards the planet where he'll be able to receive a mechanical body.

The capital of Mars, Great Syrtis. It is a deserted planet with nothing but the blowing of the red winds. Tetsuro is attacked by Geronimo, who has long dreamt of boarding the 999, and has his pass stolen by him. Ultimately, he draws his gun on his lover, Fleme.

Tetsuro is rescued from a ghost by Claire, a waitress they met. But in doing so, Claire is blasted into a million pieces. After finally arriving on Titan, one of Saturn's satellites, they go outside and Maetel is abducted. When Tetsuro goes to rescue her, oddly, he is given a gun by an old woman...

The great bandit Antares hijacks the 999 and takes Tetsuro and the gang hostage as he forces them to make an unplanned stop at his home. He takes a liking to the humans Maetel and Tetsuro and invites them into his home. But lurking in there is...

Pluto, the resting place for the bodies of those who have replaced their human bodies with mechanical ones. Tetsuro is greeted by the ice graveyard's caretaker, Shadow. She transforms herself to look like Tetsuro's mother and lures him in. She attempts to kill him, but...

Tetsuro arrives at the nest of Comets, Comet Station, and is shocked at its lack of vertical scope. He's falsely accused by a suspicious man while killing time in a bookstore and gets attacked. He goes to a doctor, but instead of receiving medical care, he tries to force Tetsuro into buying a mechanical body!

The 999 spirals downward to the bottom of gravity. They enter into the 333, which had previously crashed in there, only to find that hundreds of years appear to have passed by! The woman who controls the passage of time, a witch named Ryuz, takes a liking to Tetsuro and drags him to her home.

Continuing the plot, we find out that Ryuz is a depressed woman who was betrayed by the man she loved while she was transforming her body for him. Tetsuro sympathizes with her, but tells her, “I want to decide my future for myself.” Ryuz’s retort to those words is…

Trader Junction, a crossroads for the Galaxy Railways. Surrounding the station are countless desolate travelers with nothing more to do but wait. Tetsuro offers to treat one of the travelers to food and drinks and gets mobbed by them all. He’s rescued by a women named Hanako, but…

Tetsuro foolishly falls asleep and is taken by Hanako aboard the train bound for Wildflower Station. He is introduced to Hanako’s elderly parents as her fiancé. After seeing the delight on their faces, Tetsuro didn’t have the heart to say anything. Even the idea of throwing a wedding reception is brought up…

On the planet without a form, Nuruba, Tetsuro and Maetel are ambushed by its citizens for their bodies and their clothes are stolen. They plan to dress up like Tetsuro and Maetel and board the 999. A livid Tetsuro lunges at them, but…

The 999 has to make an emergency stop at Fossilized Planet, a place petrified all the way to the tracks. Tetsuro is curious about the fossils and leaves the 999. Suspecting that Tetsuro has intent to steal he fossils, a warrior who guards the Fossilized Planet attacks him…

Tetsuro rescues the fossilized warrior from a gang of thieves. However, the warrior runs off with Tetsuro’s pass. He attempts to leave on the 999 along with the fossil of his lover, Lidya. Just as Tetsuro follows him, the petrifying gas appears once again!

“Perfect Mechanization,” a planet where all its inhabitants have taken on mechanical bodies. All its people look down upon flesh-and-blood humans. A female doctor named Laala purposely hits Tetsuro with her car. She attempted to switch bodies with him!

On the “Black Knight’s Planet,” Tetsuro is invited to live together with the Black Knight. When Tetsuro refuses, he frantically throws his lance at him! Maetel jumps to the rescue but his his by the lance! Tetsuro stands up to the Black Knight to get revenge, but…

On the planet where people have the ability to glow, Tetsuro meets a struggling aspiring animation director named Fraiya. Tetsuro feels lousy after she rejects his offer to give her money. However, she invites him into her room and asks him to buy one of her animation storyboards.

On a planet where all living things are covered in hard armor, Maetel is hit by an armored bug and is seriously injured. Tetsuro leaves the train in search of a doctor, but there are only two people on the entire planet. Due to a misunderstanding, Tetsuro is attacked by one of them, Nutal!

In the “Mud Capitol,” a city where the rain never stops, Tetsuro receives a phone call from a woman and is dragged out into the mud. There he encounters a poor woman named Maetel who lives within the mud. She invites Tetsuro to live together with him. He refuses, however, but when he tries to escape from her mud house…

In “The Kingdom of Atonement,” a town famous for its sanitation, the conductor is attacked by a mugger on his day off! Tetsuro and Maetel console him. However, the news of the event reaches the upset Cleanliness Committee. They attempt to erase any record of the event and begin pursuing Tetsuro and the gang.

On Professional, the planet of memories, Tetsuro ignores Maetel’s advice, and makes eye contact with a professional hangman. They attempt to hang Tetsuro! He is saved by a professional gunman, only to be forced into a shooting duel!

The inside of Ballera has become hollow. Tetsuro and Maetel are swimming around in the air when they’re attacked by some cowboys and it causes a big commotion. In the Tomb of Dead leaves, they encounter Mr. Moriki, a man made from a briar bush. But then, an electric mushroom causes the 999 to suddenly stop moving!

The 999 is raided by the pirate ship Queen Emeraldas. They try to put up a fight, but realize quickly that it is all in vain, and are forced to stop on the Pirate Planet. There, the female pirate, Emeraldas, proposes a duel. Maetel loses and they set off to dispose of her body! However, the Emeraldas they faced was really a fake!

This world has been split up, due to a feud, into civilization and primeval society. On this primitive planet, the gang is attacked by the locals and Maetel is nominated Queen. Queen Maetel orders for Tetsuro to be thrown off a cliff, but it’s all part of Maetel’s plan…

The Planet of Dimension Voyage travels across the galaxy at the whim of its egotistical queen, Egoterina. The gang is attacked by Egoterina’s men, but she takes a liking to them and invites them over for dinner. However, the queen is unimpressed, to say the least, with Tetsuro’s manner of eating…

Masspron, a world covered in factories. The hotel Tetsuro is staying in is burnt to the ground. Ironically, it was deliberately caused by a young girl named Chromeria, who is leading a rebellion to get people to learn to build things while also beautifying the planet. Tetsuro manages to save her from execution, but…

Horohoro egg vendor who loses a piece of his body each time he is betrayed by his lover. He’s to the point where his chest is completely hollow with the exception of a few bones. After selling eggs to Tetsuro, he pins a crime on him as he attempts to shoot his former lover and hew new man.

On this planet where snow never ceases to fall, Maetel and a straggling Tetsuro encounter a starving girl named Yuki. She offers to take them into her house after they offer her a piece of a biscuit. There, however, the girl’s mother attempts to cut Tetsuro open. She’s thinking about using him for food…

Tetsuro and the gang touch down on the supposedly uninhabited Mirage Planet. There, they encounter the great novelist, Shosetsu Yoi. Though he had given upall attachments to the world, he becomes attracted to Maetel. He decides to abandon Tetsuro on the planet and leave on the 999.

On the Jungle Planet, the gang is captured by the alcoholic ruler, Sakezan. Maetel is chained up and forced to drink. Along with Liza, the queen, Tetsuro escapes Sakezan’s lair and leaves Maetel behind. However, he returns again and faces Sakezan!

The 999 stops on Filament, a planet filled with gas, due to interference from some ghosts. There, Tetsuro is kidnapped by a ghost parent-child duo. They are planning on using Tetsuro’s body to revive the ghost! But once they realize that he’s on a mission to get a mechanical body, they…

On the Fury Planet, a land where everyone is quick to pick a fight, Tetsuro slams into a tofu vendor as an assassin who works for Duke Mech, a friend of Count Mecha, targets him. Tetsuro feels bad for the kind-mannered tofu vendor and offers to give him some gold coins. But when he goes to leave…

The gang encounters the space warrior Edmond inside of the 999. His hometown, “Sweet, Sweet Planet” is shaped like an apple that has hadbites taken out of it. Because the ground tastes very sweet and delicious, the government has sold the land and it’s taken on a very ugly appearance. Upset by this, Edmond tried to battle the government, but…

Ulatres, a planet that specializes in screws. There, a woman named Lasen takes a liking to Tetsuro and imprisons him in the hopes of them living together. Tetsuro escapes and Lasen gives chase. However, when she sees that Tetsuro will never give up, she takes a deep look at herself…

Plated City, a planet where people are considered poor if they aren’t plated in gold. There, Maetel has her suitcase stolen by Wheel Lock, a young boy who wants to get plated. However, his mother tells him not to, so he gives up. Wheel Lock then begins to tell them about his planet…

Wheel Lock’s mother is against the tradition of plating and is trying to form a resistance. As her dying wish, she asks Wheel Lock to continue the fight against gold plating. Tetsuro goes into the heart of it all, a magnetized, plated tower. But waiting inside is…

In a ghost colony where no one is supposed to live, Tetsuro and the gang meet Dr. Cicropros and a legion of his clones. Having failed at building the colony in the past, Cicropros is using his clones to see if the colony is safe or not.

They say the planet named Mii-kun’s Mansion of Life is a flower and animal-filled planet where the souls of beloved pets of children are brought to rest. Tetsuro, mistakenly believing Maetel is being attacked, draws his gun on the animals, only to be stopped by a mysterious woman.

The 999 is in really bad shape on the Planet of the Cowardly Elder! And it’s the doing of the cowardly president of the planet who trusts no one, Delmukade. His motive is Tetsuro’s body because he lacks the courage to adopt a mechanical body.

The suitcase with Tetsuro and Maetel’s passes is stolen. However, the thief collapses while making their escape. It turns out the people on this planet have only one percent of a normal human’s physical strength. Even a gunshot from their guns barely stings. They easily get their suitcase back, but the passes are counterfeit!

Maetel is abducted by the Chief as soon as they arrive at the Spherical Housing Complex, a complex of spherical houses. There are no men here who will oppose the Chief who dwells in a castle in the sky. On the way to rescue her, Tetsuro encounters a man who looks exactly like an older version of himself, Tetsugoro Hoshino.

Within the Chief’s castle Tetsuro learns of some sort of secret and sees Maetel being subservient to the Chief. He tries to save her but is almost sent flying out into space. Tetsugoro, livid after finding out that his former lover was killed, plants a bomb on the Chief’s castle. Tetsuro has to save Maetel in the five minutes before the bomb detonates!

As they approach the station, the Face of Memories, a woman passenger named Female causes a disturbance on the train and derails the 999. However, it seems that she knew the Conductor when he was young. As if to anger the Conductor on purpose, she slaps Maetel. An angry Conductor takes a gravity control device that derailed the train…

Tetsuro has his pass stolen on a planet where the wind never stops blowing. Tetsuro believes the thief to be a young man named Kira but Kira denies any wrongdoing. The next day, Kira shows up in front of Tetsuro, confused. He says he wanted to steal the pass so he could board the 999. But Kira’s father who should be crying, apologizing for his son, is actually…

At Deadwood Mountain, a young man named Prider arrived on a train in order to make money for his girlfriend Alice by music. Tetsuro feels bad for his girlfriend, but doesn’t say so. He gets angry at Prider, who never stops singing. While fighting, Tetsuro remembers how he got his pass from Maetel. Just then, the 999 is taken over by a horrible mother-and-daughter duo known as Valkyries.