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.

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.

The 999 arrives on a planet where the entire populace except for one person have been turned to stone by a petrification cloud. 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.

Additional people arrive on the planet who seek to steal the petrified remains of the warrior's lover. Moreover an another petrification cloud is approaching the planet.

The 999 arrives at the Dual Planets, a world full of machine people. When a large group of machine people at a restaurant treat Tetsuro and Maetel rudely, Tetsuro goes on a rampage and kills them all. Tetsuro and Maetel then meet Lala, a machine woman who steals Tetsuro's body, switching it with her own.

The 999 is pursued by the Black Knight, a caped figure in a dark, fog drenched world. The Black Knight requests Tetsuro stay on the planet and be his friend, but Tetsuro refuses and he attacks. They then travel to the planet Yonde 3 where the son of an innkeeper, a musician, desires Tetsuro's pass so he can leave the planet.

On their latest planet, Tetsuro meets Freiya, a poor girl who appears beautiful to him but is considered ugly and deformed by the other inhabitants of her planet because she does not glow in the dark with a uniform light. Freiya is an amateur animator who hopes to become a director someday.

The 999 arrives on a planet where everything is encased in armor, including a panzer beetle that severely wounds Maetel. Tetsuro travels the planet, searching for a doctor who can help her. The doctor however is too old to help, and his son, who is the only other person left alive on the planet tries to kill Tetsuro.

The 999 arrives on a planet containing a large mud pit that Maetel warns Tetsuro to not go near. When he does, Tetsuro is dragged into the pit and forced to live in a bubble with a woman who also calls herself Maetel.

The 999 made a two-week stop to the Planet of Confession, a world supposedly free of all evils. While the conductor decided to take his holidays on the planet, a robber appeared and took all of his money. The incident was made aware by the "Cleaningless Committee". Instead of catching the perpetrator, the committee decided to uphold the planet's reputation by trying to silence the three travelers.

The 999 travels to a planet full of professionals, and Maetel warns Tetsuro not to look anyone in the eye. When Tetsuro does so, he is captured by a professional hangman who tries to hang Tetsuro. Tetsuro is saved when another professional, a gunman arrives and shoots the hangman. This professional however insists on teaching Tetsuro to become a professional dueler.

The 999 arrives at a hollow planet with no gravity; as a result everything is a lot fatter looking, and can float through the air. Tetsuro and Maetel are confronted by cattle keepers but are able to escape. As they travel to their next planet Tetsuro meets an artist who has a wooden machine body. When they travel through a planet full of leaves, an electric mushroom threatens to destroy the train.

The 999 is attacked by the pirate ship Queen Emeraldes, which forces the train to a pirate planet. There Tetsuro and Maetel are captured by the pirate Emeraldes, a caped woman who desires Maetel's body.

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.

The 999 finds its next destination destroyed; it was demolished by a planet that travels through the dimensions, smashing other planets. When the 999 lands on this planet, they are confronted by the planet's ruler, Egoterina.

Tetsuro meets Clowmaria, a freedom fighter on a heavily industrialized world that is trying to get the people of her planet to change their ways.

Tetsuro meets Horohoro, a poor skeleton man who has lost most of his body including his ribs because he is so poor.

After the 999 landed on the five-planet system Snow Capital, Tetsuro and Maetel explored the city. He fell through a hidden hole which led him to the slum part of the city, and was promptly mugged by a group of local residents. Tetsuro spotted a girl, Bojin Yuki, to whom he gave his last bit of biscuit. Yuki then brought him to her home on the surface. Yuki's mother, however, wanted to cook Tetsuro for food.

The 999 arrives on a planet where Tetsuro and Maetel meet an old writer who lives alone and has extremely long hair. The old man steals Tetsuro's pass and flees on the 999 with Maetel, leaving Tetsuro on the planet.

Sakezan is the only human living in a jungle world named after him. He is a parody of Tarzan and, as his name suggests, is very fond of saké. Sakezan captured Maetel when the 999 took a quick stop there and she became her slave/companion. In an attempt to rescue her, Tetsuro was defeated by Sakezan and ended up in a prison cell.

The episode opened with the story of the post-modern feudal world of Filament, which was destroyed when its sun went supernova. An energy cloud formed where the planet used to be, and its inhabitants, not accepting their untimely fate, became spirits. When the 999 passed through the energy cloud, the ghosts disabled the train and kidnapped Tetsuro. One of the spirits wanted her son to possess Tetsuro, so that he (the spirit) could travel to the destination and receive a mechanical body.

The 999 arrives at a planet where people are passionate and don't hide their emotions. Meanwhile a group of 4 assassins are hired by a friend of Count Mecha's to kill Tetsuro.

Tetsuro meets Edmund, a fellow passenger on the 999 who is looking forward to returning to his homeworld on their next stop. When they arrive however the planet is completely ravaged.

The 999 arrives on the planet Ulatorus, which contains mountains of screws. When a storm causes one of the mountains to collapse, Tetsuro loses his pass and meets a machine woman who kidnaps him, seeking to keep him in her home permanently. At the same time, the 999 malfunctions due to a faulty screw.

The 999 arrives on a planet where everything is plated in gold, the streets, the buildings, even the people. A thief knocks Tetsuro out and steals Maetel's luggage. Tetsuro runs after him into the sewers where he discovers the thief, a teenage boy named Hoilock, is not gold after all.

Hoilock's mother's dying wish is for him to continue in her footsteps in toppling those in charge of making everything gold. Meanwhile the 999 takes off without Tetsuro when he doesn't return in time.

The 999 stops at an abandoned artificial colony world. Tetsuro is pleased with its appearance but Maetel is puzzled that the colony looks quite different than it did on her last visit. They investigate further, and are set upon by a terrified mob of physically identical men. Maetel recognizes their face as being that of the colony's architect, Dr. Cyclops.

The 999 approaches the planet Mīkun's Mansion of Life, and all the passengers appear depressed, closing the blinds as they approach it. When Tetsuro and Maetel arrive at the hotel, Tetsuro finds a tiger and snake in the hallway, so he hides in his bed the rest of the night. The next day Maetel introduces Tetsuro to Mīkun, who takes care of all the various animals on the planet, which are actually all dead animals beloved by their master.

The 999 is heavily damaged and forced to land on a planet under the despotic rule of the Cowardly Elder, President Delmukade. Tetsuro, Maetal and the Conductor are forced to travel underground where they meet Delmukade, who demands that Tetsuro sell him his young body. Delmukade's son Paschal arrives, and reveals that Delmukade is the only person living on this planet; suspecting rebellion everywhere, he had killed everyone else including Paschal's mother.

The 999 arrives on a planet where everyone is very beautiful, but also extremely weak, not even going outside during the day due to the sun. A couple steals a suitcase containing Tetsuro and Maetel's passes, but they pass out from running and when they shoot Tetsuro, it is too weak to harm them. They still manage to switch Tetsuro and Maetel's passes with fake ones though, and board the 999.

The 999 approaches a large group of spherical homes, which are ruled by a Great Chieftain. Upon entering, Maetel is captured by the Chieftain's minions. Tetsuro meets Tetsuguro, a man who looks just like him and has assembled weapons to defeat the Chieftain. While they head to the Chieftain's castle however, Tetsuro is tricked by a scarecrow of Maetel and is shot.

Tetsuro is captured and brought before the Great Chieftain, who has a computer with all of Maetel's secrets. Tetsuguro manages to rescue Tetsuro, and discovers that his girlfriend has been killed by the Chieftain.

The 999 approaches the planet Visage of Memories, where the Conductor many years ago promised his lover, Marvelous, that he would make money on the 999 and return. A new passenger, Fimel boards the 999 and treats the Conductor very rudely, then causes the train to derail with a device worn around her waist.

The 999 arrives on the planet Arashigaoka (lit.: Windy Hill) where a sickly father and son, Kira operate a shoe repair store. Tetsuro's pass is stolen by the father, who seeks to get on the 999 and leave the planet so he won't be a burden to Kira. Kira forces him to return it at gunpoint, who wants to obtain a pass for him legitimately.

At the 999's latest stop, Deadwood Mountain, Tetsuro and Maetel meet Prider, a poor singer who seeks to board the 999 so he can become a famous singer. When Prider doesn't have enough money to board, he borrows money from his girlfriend Alice and buys a ticket on the 999. Tetsuro gets upset at Prider for abandoning his girlfriend after all she did for him. The 999 is approached by the Valkyries, a group of witches, and three of them board the train.

The three Valkyries bring everyone aboard their ship, where our heroes meet their mother, the head Valkyrie. The ship travels to the edge of the universe where the Valkyries show our heroes the bones of all the humans they've killed.

Nanmi, a passenger on the 999 is able to convince the train to head to his planet, El Alamein, when he threatens to kill Tetsuro. Once they arrive Tetsuro and Maetel travel outside with him. The planet is mostly a desert, with many inactive tanks lying around. Sensing their life however, the tanks come back to life and attack.

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.

At gunpoint (from the previous episode), Tetsuro told Zeda of his struggles back on Earth. Zeda was instead moved and decided to joined the rebels. With his companions Santana and Brudas, Zeda managed to unite the two soldier factions and started to attack government facilities.

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 at the ghost tunnel, a giant tunnel in space formed by giant black orbs. An android woman, Eroze appears and asks Tetsuro to come off the train. When he refuses, she attacks the train with the orbs until he relents and agrees to come out.

As the 999 approaches its next destination, a large number of small blue blobs start passing by the 999, warning it to not go any further. Eventually the 999 gets stuck in a larger version of these blobs, which apparantely is their mother. The Galaxy Railways headquarters gets ready to blow it up so the 999 can go on, but all of a sudden a ship crashes into the blob.

After being brought aboard the 999, Artemis reveals her history, how she departed her mother to acquire a humanoid machine body. Having to work to pay it off in a factory had its toll however, and she stole a ship and fleed. Artemis dies soon after and is brought to the heart of her mother, where she is absorbed into it. With Galaxy Railways headquarters planning to destroy the mother, Tetsuro cries out for them to not do it.

A boy who looks just like Tetsuro, named Manabu, and his brother work hard and are able to purchase a single pass for 999. The brother passes away before they can make it to the town where 999 arrives. When Tetsuro goes out on his own, Maetel mistakes Manabu for him. Tetsuro arrives and fights Manabu, but they quickly become friends as they have so much in common. When Manabu tries to board the 999 however, he is told that the pass is counterfeit.

The 999 arrives on the Planet of the Endless Summer, which is populated by humanoid insect like creatures. The queen of the creatures captures Tetsuro and Maetel, planning to boil them to make them food for her children.

The insect babies hatch and when Tetsuro finds himself unable to kill them, they climb aboard the 999 and start eating it.

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.

Tiny changes his mind about going on the 999 and decides to stay on his planet with his girlfriend until they can both get tickets. The two of them help Tetsuro and Maetel when they are confronted by the planet's natives.

Tetsuro and Maetel arrive on the planet Footsteps Village, and are told of evil spirits that possess and kill people. Tetsuro is warned to not go out at night, but when he meets a spirit that takes the form of water, he does it anyway.

The 999 stopped on the planet Idle One's Mirror, where everything is automated by machines. Tetsuro disembarked the train alone, and was taken by an automated taxi around the city. Once the taxi brought him to a residential area, he found out that the all residents are obese from the lack of physical work.

The next stop for the 999 was the Planet of Tomorrow, a peaceful world whose inhabitants had no knowledge of space flight. The 999 and its passengers were to land in secrecy. A group of youths, led by Taro and Hanako, anticipated for its arrival. While the group only wanted to publicize the train's existence, Taro wanted to board the train. In doing so, Taro stole the train passes and spending money from Tetsuro and Maetel, as well as Tetsuro's clothes. In their plight Tetsuro and Maetel managed to find lodging in a small hostel (i.e., the pint sized room), where Tetsuro befriended the struggling comic-artist Adachi, who had been looking for an inspiration for his work. The episode ended with Taro offering Maetel's pass to Hanako, who refused it.

While stranded on the planet without train passes, Maetel sought help from Galaxy Railways, but her efforts ended in vain. Meanwhile, with Adachi's help, Tetsuro found a job at a noodle shop to support himself and Maetel. Tetsuro and Maetel ran into the disguised Taro when they returned to the train station. Taro, not wanting to leave his friends behind, gave the passes to them, not knowing at first, that they were the rightful owners. As the train departed, Taro returned to Hanako and their friends. And Adachi, who also saw the train leave the planet, finally found inspiration for comic.

As the 999 approaches the City Without Night, Maetel tells Tetsuro of a lake there, but tells him not to go out to see it. When they arrive on the planet, Tetsuro gets in trouble for going out at night, but is saved by Maetel. They are told that no one is allowed out at night because of a dangerous dinosaur, Heron, that lives in the lake. Tetsuro and Maetel head there anyway and help Heron when it is captured by some photographers. Heron actually is a friendly creature, and later helped Tetsuro and Maetel out when the police try to arrest them for the death of the photographers.

The 999 stops at the Pitch Dark Planet, where all light is instantly absorbed. A while after Maetel leaves the train to "attend to private business", Tetsuro is beckoned outside by a figure at his window, who proves to be Miru, a daughter of the planet's ruler. She and her father tell him that Maetel has been kidnapped by Miru's sister Lelan, a deranged but brilliant scientist who plans to use Maetel's brain to launch an artificial sun into orbit, and that Maetel will die unless Tetsuro can infiltrate Lelan's base and kill her. Further, the new sun will doom most of the life on their world, which has never had light in its entire natural history. Tetsuro goes back for his gun, but is taken prisoner by Lelan the instant he steps off the train. His efforts to escape prove futile and Lelan launches the sun. Miru, horribly burned, staggers into the base and tries to shut the sun off but is shot by her sister. Maetel accosts Lelan and accuses her of genocide but she retorts that sacrifices must be made for the greater good. She runs out into the sunlight and is burned to death. As the train leaves, the Conductor reports that 99.99% of the planet's population has perished.

Maetel and Tetsuro arrived at the Planet of Silence, where raising one's voice (beyond a whispering level) was punishable by death. Maetel asked Tetsuro to stay behind while she had to attend to some private business (concerning her "mission" with Tetsuro). Bored and worried, Tetsuro went looking for her. The townsfolk could not tolerate his voice, and was soon caught by the authorities to be executed. He was rescued by Maetel and a woman named Sylvia (in a Good, Bad, and Ugly way). Sylvia revealed that the law was enacted because everyone wore hearing aid to better listen other people's business, a vestigial legacy of a former totalitarian regime. Sylvia's father was executed when he cried for help to save her, when she was still a baby. They were discovered and surrounded. Knowing their weakness, Testuro screamed at the crowd so loudly, that their hearing devices fell out. The planet returned to normal as the train departed with Maetel and Tetsuro on board.

The 999 arrives at a planet where the people are starving because the Queen of the planet orders all food to be brought to her. Tetsuro and Maetel travel to the island where the Queen is located and find that she died long ago, with her consciousness stored in a device behind her corpse. Tetsuro destroys the device and her corpse, freeing the planet from her oppression.

As the 999 touched down on the Funeral Planet, its arrival (and whistle) disturbed a funeral procession, who decided to bury Maetel and Tetsuro alive as punishment, with the proper pomp and circumstance. They were rescued by Machiru, a woman responsible for ringing the funeral bell. She explained that the inhabitants on the planet were immortal, so killing for funerals became a past time when they witnessed one over 120 years ago, when a couple crash landed on the planet. The bell stopped ringing, and Machiru was killed by the procession as a result. Maetel and Tetsuro came across the procession and stunned them all. Maetel explained to Testuro that funerals would be given to them when they stopped moving, whether they were still alive or not.

Dairuz, a monk with a mechanical body was on board of the 999. His rang his bell throughout, and the sound waves were powerful enough to damage the train and all of Tetsuro's teeth. The Conductor took the train to the Medical Treatment Asteroid for an overhaul as a result. Maetel and Tetsuro met Maria, who brought her boyfriend Mikhail for gunshot treatment from their homeworld, the crime-ridden Asteroid 33. The operation was successful, but Mikhail was losing his will to live. Dairuz tried to save him with prayers, but it was Tetsuro who gave Mikhail hope to live on. Despaired, the Dairuz smashed his bell, and sacrificed part of his body so that Tetsuro's teeth could be fixed. In parting, Dairuz, who was now attached to a rock to sustain his body, told Tetsuro he had to remeditate to change his way of salvation.

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 episode opened with an armed robbery that took place on the 555 when it took a stop on the Medical Treatment Asteroid (in Episode 67). Next, the 999 received an emergency stop signal and the Conductor halted the train in mid-space. Maetel was summoned by the C62 (the locomotive for the 999), who informed her that it was going to disconnect and go on its own. News of both incidents reached the Galaxy Railways Headquarters, and one of the operatives determined that both trains were on the asteroid when the heist occurred. The Conductor later discovered that the two robbers were on board the 999, and soon after the SDF appeared. One of the robbers took Tetsuro hostage and demanded that the SDF be attached to the 999. While the 999 continued with its journey, the C62 returned and attached itself to the train. Tetsuro and Maetel used the opportunity to pacify the two perpetrators and handed them over to the authorities. At the end, Maetel revealed that the the emergency stop was a test of Tetsuro's patience, and that the C62 was also part of the plot in bringing the boy to Andromeda.

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.