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.

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 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 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 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.

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 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 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.

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.

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.

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 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 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 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 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.

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.

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.

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.

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.

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A remake of episodes 51-52 of the TV version.