The Cuckoo explores the theme of tragedy occurring in an upper-class marriage. Namiko is the daughter of a general. Takeo is a Naval officer, son of a baron now deceased. At first, they are happily married. Then three sources of unhappiness ruin it all. The first is Taneo, Takeo's cousin and Namiko's rejected suitor. Then there is Namiko's cruel and demanding mother-in-law. Finally, Namiko contracts tuberculosis. Takeo's mother urges him to divorce Namiko, whose illness prevents her from having children. Takeo is torn between the absolutism of the family and individual moral authenticity. Even though it means the end of his lineage, he refuses to take a course of action he considers inhumane and unethical. Takeo's choice is dramatically enhanced by the outbreak of the First Sino-Japanese War. He is called up for active duty, leaving Namiko unprotected. His mother, encouraged by the vengeful Taneo, takes matters into her own hands. She in effect dissolves her son's marriage by sending his wife back into her family. Takeo attempts to die in battle, but is only wounded. Namiko considers throwing herself into the sea, but is stopped by an old woman who brings her a copy of the Christian Bible, which they discuss. She dies of her illness, and the novel ends with her father and her former husband meeting and mourning at her grave.

In the original Japanese, the story is divided into three books, each with many short, unnamed chapters. Translations into other languages combined these chapters together and assigned titles to them.