This novel is split into two sections titled Summer and Winter, set in their respective seasons.
The novel begins with the main character, Noboru finding a hole in his chest of drawers that allows him to look into his mother's room undetected. He swears to never do anything to attract the grown-ups' attention to the chest, and spies on his mother through the hole. Noboru is also annoyed that his mother locks him in his room nightly to prevent him from sneaking out after he was caught once before.
Fusako had taken Noboru to a ship as Noboru is very interested in them. Onboard, they meet Ryuji, a sailor and second mate aboard the commercial steamer. It is revealed that Ryuji has strong but vague notions of a special honor awaiting him at sea.
Fusako and Ryuji develop a romantic relationship with the fully support of Noboru. Noboru idolizes Ryuji and hails him as a hero. He spies on them through the hole in his chest on the first night they have sex.
Noboru reveres Ryuji, but a chance encounter on the second day of their acquaintance changes this. That morning, Noboru had lied to his mother about his whereabouts to meet his gang. His gang is led by a 'Chief', and five other boys who are not referred to by their names, but by their respective numbers. Noboru is 'Number Three'.
That day, Noboru and his friends had captured and gruesomely killed a tiny stray kitten to practice "objectivity" and "absolute dispassion" whereby they attempt to rid themselves of emotional responses. On the way back, the boys meet Ryuji.
Before seeing Noboru, Ryuji had doused himself with water to combat the summer heat. He is very friendly to Noboru, which Noboru feels is undiginified. Noboru thinks his behavior is not compatible with that as a hero. However, he is thrilled once again when Ryuji recounts his voyages around the world.
When Ryuji's ship sets sail again, he leaves. However, he continues to exchange letters with Fusako and they fall deeply in love.
In the second part of the novel, Winter, Ryuji returns and meets up with Fusako and Noboru. He decides to abandon his life as a sailor and proposes to Fusako. She agrees, and they decide to marry. However, this estranges him from Noboru, whose gang resents fathers as a terrible manifestation and as a 'villain'.
Ryuji and Fusako announce their engagement over dinner. Noboru is horrified, but does not tell them nor show it in his face. He pretends to be happy with the arrangement. Later, when the three of them return home, Noboru spies on them in his peephole. However, his mother discovers him in his position and his horrified. She demands that Ryuji punish him, but Ryuji does not. instead, he decides to take a paternalistic approach in talking it through with Noboru, stating that someday, the three of them will look back and laugh at this event.
Instead of being relieved for escaping punishment, Noboru is horrified. He feels that Ryuji's approach is that of a father figure, a position he and his gang feel is 'malicious', with the sole aim of suppressing freedom and promoting conformity to society. He realizes that Ryuji has become a 'father', and therefore has lost his glory. In Noboru's perspective, Ryuji has changed from a 'hero' to a 'villain'.
Noboru brings up the issue with his gang, and the Chief decides that they have to kill Ryuji to restore his glory. The gang leads Ryuji to a remote location where they ask him to recount his stories at sea. Ryuji reminisces over his adventures as he drinks a poisoned tea the boys have given him. The novel ends there, whereby it is not explicitly said, but implied that the boys murder being carried to completion.