the story follows giovanni, a poor young boy who is outcast and bullied by his peers due to his timid nature and his missing father. his only friend among them is named campanella. in class, the teacher asks what the milky way is composed of. giovanni knows the answer; he read about the galaxy with campanella, but he's too shy to speak up. when called upon, campanella doesn't say the answer either.
in the evening, the rest of the town is preparing for the festival of stars. giovanni goes out to pick up milk for his mother, and runs into his classmates again. they mock him, and he runs away until he finds himself at the top of a hill. he lies there and watches the stars above, away from the noise of the town and the harassment of his peers. suddenly then, he hears a train, and a conductor calling out to him. he gets on the train, and after some time he notices another passenger: campanella! he says that everyone else ran to try and catch up, but he was the only one who made it in time.
at the start of the northern cross and the pliocene coast chapter, campanella suddenly asks: "i wonder if my mum will ever forgive me." he says he would go to the ends of the earth to make her happy, but can't figure out what would make her happiest. he then says "people create happiness when they do something good," and is sure his mother will forgive him.
the boys explore the milky way together on the train, seeing breathtaking sights: on the pliocene coast, they find a riverbed with gleaming sand and quartz and topaz stones on the bed, with giant walnuts growing from the ground and archaeologists digging out the skeleton of an unknown beast; when they get back to the train, they meet a birdcatcher who tells them about the herons made of congealed sand from the milky way and gives the boys part of a goose to eat (they taste just like cake). when the birdcatcher asks where they came from, neither of them can remember.
the train leaves swan station, and more passengers come onto the train: a young boy, an older girl, and a young man. the girl, kaoru, asks where they are, and the young man says they are on their way to heaven. the three of them had come from a ship that hit an iceberg, and they had died. giovanni wonders what he could do to make the man happy, and the lighthouse keeper on the train says that "so long as you're on the proper road, no matter how trying a thing may be, you'll be getting closer, one step at a time, up and down the high points and the low points to real happiness." the lighthouse keeper offers everyone apples, which they accept.
campanella starts to talk with the three from the ship, about magpies and peacocks outside of the train, and giovanni finds himself getting upset as campanella pays less attention to him. he thinks, "is there really nobody who will stick with me to the edges of the universe and beyond? campanella just sits there jabbering away to that little girl, and it hurts me more than anybody knows." he tears up, feeling alone.
they pass the constellation of scorpio, and kaoru tells the story of the scorpion: the scorpion lived his days killing and eating other bugs, and one day was caught by a weasel. he escaped, but fell down into a well with no way to get back up, and so he prayed to god to look into his heart and use his body for the happiness of others. with that, he turned bright red and lit up the darkness of the night, becoming the constellation.
the train reaches the southern cross, and the young man tells the children it's time to leave. it's where they get to go to heaven. giovanni wants them to stay, but kaoru simply says they have to leave, because god says so. giovanni says, "a god who says that is a phony god." they argue over which god is phony, which one is the real god, and the young man says "let us pray that we will all meet someday in the course of time before that real god." giovanni and campanella are alone again.
"campanella," said giovanni, sighing deeply, we're alone again. let's stay together till the ends of the earth, okay? if i could be like that scorpion and do something for the benefit of all people, i wouldn't care if my body burnt up a hundred times over."
the train passes the coalsack nebula, a hole in the sky. giovanni peers into it and sees nothing but darkness. beyond that, campanella sees a field, the most beautiful field he has ever seen, with his mother sitting there -- he sees the real heaven. when giovanni looks, he sees nothing but blurry whiteness where campanella was pointing. "campanella," said giovanni, turning towards him, "we're going to stick together, okay?" but there was no campanella where campanella had been sitting, only the black shining velvet seat.
everything goes black and giovanni finds himself in the grass on the hill; he had fallen asleep. he runs down and goes back to pick up the milk for his mother, and finds commotion back in town. while giovanni was asleep, campanella had fallen into the river after zanelli had fallen off his boat. campanella pushed zanelli back out of the water, but no one could find campanella. giovanni was the only person who knew where he went.