The story opens on the unnamed narrator, who has just read in the newspaper that his little brother Sonny was arrested for using and selling heroin. Throughout his day, he cannot think of anything else. He’s a high school algebra teacher, and he looks at his young students, wondering which ones are, like Sonny, turning to drugs to escape the suffering of their lives as young black men in Harlem.
The narrator runs into an old friend of Sonny’s—a drug user—on the way to the subway, and their conversation makes the narrator understand how hard prison will be for Sonny. Still, the narrator says he doesn’t plan to do anything to help Sonny, though he gives Sonny’s friend money when he asks.
The story jumps ahead to months later, when the narrator’s young daughter Grace has just died of polio and the narrator finally, in his grief, decides to write to Sonny in jail. Sonny replies that he needed to hear from his brother, but didn’t want to reach out first because he knows the pain he has caused. The two strike up a correspondence, and when Sonny is released from jail he comes to live with the narrator’s family in Harlem.
Having Sonny around seems to trigger the narrator’s memories of his childhood, and the story jumps back in time. The narrator recalls that right after his father died, his mother made him promise not to let anything happen to Sonny. The narrator didn’t understand her worry, so she told him about how his father had watched his brother (a musician, like Sonny) get run over by a car of drunk white men. The narrator’s mother reminds him that he has a brother too, and the world hasn’t changed.
When the narrator’s mother dies soon after, he gets a furlough from the army to attend the funeral. The narrator is married to a woman named Isabel, and he arranges for teenaged Sonny to go live with Isabel’s parents until he finishes school. During this visit he has a conversation in which Sonny reveals his desire to be a jazz musician, and the narrator discourages him harshly. Living with the narrator’s wife’s family, Sonny plays their piano day and night. Eventually, after the family learns he hasn’t been going to school, Sonny joins the navy and leaves without saying goodbye. The next time the narrator sees Sonny is after the war. Sonny is living downtown with a group of musicians. The narrator and Sonny have a horrible fight, and they don’t speak again until the narrator writes to Sonny in jail.
The story then returns to the present, when Sonny has been living with the narrator for two weeks. The narrator is home alone watching a revival meeting across the street, and he sees Sonny at the edge of the crowd listening to them sing. Sonny comes upstairs and invites the narrator to hear him play in the Village that night. The narrator agrees to come, and they discuss the woman singing across the street at the revival meeting. It triggers a conversation about the intensity of suffering, and how drugs and music can be an escape from it, a way not to be shaken to pieces by the world. Sonny reminds the narrator that, while he is clean now, his troubles aren’t necessarily over, and the narrator silently promises to always be there for Sonny.
The two of them go to the nightclub, and the narrator is surprised by how admired and beloved Sonny is by everyone there—Sonny has his own world that the narrator doesn’t know anything about. Sonny and his band begin to play, and the narrator thinks about how rare it is to have an experience where music touches you. That leads him to reflect on how difficult it must be to play music, to have to impose order on all the rage and delight and confusion inside of people. Sonny seems to struggle at first to really put himself into the music, but eventually Sonny hits his stride and the narrator, listening from a corner, tears up thinking about suffering: his own, Sonny’s, their parents, and the suffering in the world around them. He realizes that music is telling everyone’s story, and that it’s a gift to strive to tell it anew in a way that will make an audience listen and make them confront their demons in a way that makes them feel less alone.
When the band pauses, the narrator buys Sonny a drink and the bartender puts the glass on top of his piano. Sonny sips it, meets eyes with the narrator, and returns to playing. The narrator watches the glass shake sitting on the piano above Sonny’s head, comparing it to “the very cup of trembling.”