"A Family Supper" begins with an explanation of fugu, a poisonous pufferfish that can be lethal when improperly prepared. The narrator says his mother died from eating fugu prepared by a neighbor. He had been living in California at the time, and because contact with family was severed, he didn't learn of his mother's death until he returned to Japan two years after it happened.
The narrator recounts how his father told him on the drive from the airport to the father's home in Kamakura, south of Tokyo. The father is a strict traditionalist who is proud of his pure samurai bloodline. Their conversation is strained as they discuss the failure of his father's business firm, the disgrace of which precipitated his business partner's suicide.
Once they are at the family home, they briefly discuss how the father believes the narrator was led astray, but no longer thinks he is evil. They do not directly address the issue, agreeing to let the subject drop.
The narrator's younger sister, Kikuko, arrives. She is happy to see her brother but shows her emotions in a restrained way around their father. Only when she and her brother go into the garden for a walk does Kikuko relax. She reveals that she now smokes cigarettes and has a boyfriend who wants her to go hitchhiking in America with him. The brother says he doesn't see why she shouldn't. Kikuko tells her brother that their father's business partner didn't just kill himself, he also turned the gas on kill his wife and children in their sleep. She says it's sick. At an old well in the garden, the siblings discuss how the narrator once believed he saw the ghost of an old woman in a white kimono staring back at him from a clearing by the well.
At the house, Kikuko hesitantly obliges her father when he tells her to take over the cooking. The father leads the narrator on a tour of the house, remarking on the large empty place, which the father says is too big for him to live in alone. The father picks up a model of a battleship he is building. He casually mentions how he believes his wife didn't just die because of the fugu, saying she had many worries and disappointments—a reference to the pain the narrator put his mother through.
Over supper, the father continues asking his son what his plans are, and whether he is going to stay in Japan. The narrator has not decided yet, but says that there is nothing for him in California now that his relationship is over. Toward the end of the meal, the father opens a large steaming pot of fish. They each take turns serving themselves, and eat together. The narrator remarks that the fish is good and asks what it is. The father replies that it is just fish.
They finish eating and the father tells Kikuo to make tea. She obliges while the men sit in the tearoom. The narrator asks his father about his partner killing his family before killing himself. The father suggests his partner was too devoted to the business and that devotion warped his mind. They agree with each other that it wasn't right to do what he did. The father says there are other things in life aside from business.
The story ends with the father inviting the narrator to live in the house with him. He adds that Kikuko might want to return to the house after she finishes university in the coming spring. The narrator thanks him but doesn't give a definite answer to the request. They fall silent and sit waiting for Kikuko to bring them tea.
