On the day of a large festival, Giovanni meets his classmate Zanelli. He makes fun of Giovanni and runs away to the festival. Giovanni can not go to the festival because he has to take care of his mother.
Tired, Giovanni lies down on top of a hill. He hears a strange sound, and he realizes he is sitting in a train with Campanella. The train travels through the Northern Cross and other stars in the Milky Way. Along the way, the two see fantastic sites and meet various people—scholars excavating a fossil from the white sands of crystal and a man who catches herons to make candies from them.
Children who were on a ship that crashed into an iceberg (possibly Titanic) get on the train at Aquila, suggesting to the readers that the train is transporting its passengers to their afterlife. The train arrives at the Southern Cross and all the other passengers get off the train, leaving only Giovanni and Campanella in the train. Giovanni promises Campanella to go on forever, together. But as the train approaches the Coalsack, Campanella disappears, leaving Giovanni behind.
Giovanni wakes up on top of the hill. He heads to the town, and finds out that Zanelli fell into the river from a boat. He was saved by Campanella who went into the water, but Campanella had not come up since then and is missing.
A tribute to those who give themselves to others is a recurring theme throughout the storyline, and according to Hasebe (2000), they are reflections of Kenji's philosophy of self-sacrifice, a view appearing in many other juvenile novels of his such as Yodaka no Hoshi and Gusukōbudori no Denki. Meanwhile, Suzuki (2004) interprets them as representing a "holistic thought of Ecosystem".
The most prominent but controversial alteration made in the anime is that the main two characters (and their classmates) are depicted as cats. Some other characters such as the children from the ship are humans.
Many members of the anime staff ultimately went on to high-profile careers as directors or as studio founders, such as Kōichi Mashimo, then a storyboard artist, who more than ten years later would go on to form the famed studio Bee Train.
The captions throughout the film is in Esperanto, paying homage to Kenji Miyazawa who was strongly interested in the language. In the language, the film is called Nokto de la Galaksia Fervojo. Texts appearing in various scenes are also written in Esperanto, such as writings on the blackboard in the classroom. An apparent extra at press in the printing house—where Giovanni works—tells the shipwreck of a passenger ship, carrying the Esperanto lyric of "Nearer, My God, to Thee".
A part in a 2002 play consisting of various works by Kenji written by Yutaka Narui for a theatrical company Caramelbox, features the story by the name of . It follows through the episodes in the novel rather briefly. The play also includes some lines by Professor Burukaniro, which appear only in the first three versions of the novel.
This book is also heavily mentioned and referenced in the anime Hanbun no Tsuki ga Noboru Sora (Looking up at the half-moon), as a book that Akiba Rika's father gave to her.
A character in the light novel .hack//AI buster remarks that he took his online handle, Albireo, because he was so affected by Miyazawa's description of the binary star Albireo. The book is referenced once more during a discussion on how much stories can change from the first draft to the final draft, due to the various different versions of Night on the Galactic Railroad.