The short story concerns Franny's weekend date with her collegiate boyfriend, Lane Coutell. He takes her to a fashionable lunch room, where he is described as “monopolizing” the conversation and trying to impress Franny with his news of receiving a suggestion to publish his latest paper on Flaubert. Franny appears upset, questioning the importance of college education and the worth of Lane's friends. She eats nothing, feels faint, and becomes progressively more uncomfortable talking to Lane. Eventually she excuses herself to visit the restroom, where, after a crying spell, she regains her composure.
She returns to the table, where Lane questions her on the small book she has been carrying. She responds nonchalantly that the book is titled The Way of a Pilgrim and tells the story of how a Russian wanderer learns the power of "praying without ceasing". The Jesus Prayer involves internalizing the prayer "Lord Jesus Christ, have mercy on me" to a point where, in a manner similar to a Zen koan, it becomes unconscious, almost like a heartbeat. Lane is less interested in the story than in keeping their timetable for the party and football game, though when Franny faints, he tends to her and postpones the weekend's activities. After she wakes, he goes to get a taxi, and leaves Franny alone—practicing the act of praying without ceasing.
Zooey, smoking and soaking in a tub, is reading a four-year-old letter from his brother, Buddy. His mother, Bessie, enters the bathroom, and the two have a long discussion, centering upon Bessie's worries about his sister, Franny, who is in a state of emotional collapse. During the conversation, Zooey verbally spars and banters with his mother and repeatedly requests that she leave. Bessie tolerates Zooey's behavior, and simply states that he's becoming more and more like his brother Buddy and wonders what has happened to her children that were once so "sweet and loving".
After Bessie leaves, Zooey gets dressed and goes to the living room, where he finds Franny on the sofa with her cat Bloomberg, and begins speaking with her. After upsetting Franny by questioning her motives for reciting the "Jesus Prayer", Zooey retreats into the former bedroom of his two older brothers, Seymour and Buddy, and reads the back of their door, covered in philosophical quotations. After contemplation, Zooey telephones Franny, pretending to be Buddy. Franny eventually discovers the ruse, but she and Zooey continue to talk. Knowing that Franny reveres their eldest brother, Seymour—the psychologist, spiritual leader, and confidante of the family, who committed suicide years earlier—Zooey shares with her some words of wisdom that Seymour once gave him. By the end of the call, as the fundamental "secret" of Seymour's advice is revealed, Franny seems to find illumination in what Zooey has told her: “there isn’t anyone out there who isn’t Seymour’s fat lady” and that the “Fat Lady” is Christ himself.