The narrator reads about his brother's arrest in the newspaper while on his way to work. He spends the whole day in shock thinking about Sonny and his drug problem.
He doesn't contact Sonny right away. In fact, he doesn't write to him until his daughter dies. Once they reconnect, though, they start writing each other often. When Sonny gets back to New York, he ends up moving in with the narrator and his family. The narrator worries that he's just putting Sonny back into the same situation that turned him to drugs in the first place.
Upon seeing Sonny again, the narrator starts to recall his childhood with Sonny. He remembers a specific conversation he had with their mother before he went into the army. She tells him that their father had a brother who was killed when a car full of white men intentionally ran him over. The narrator never knew he had an uncle, and his mom tells him this story so that he'll always be there for Sonny.
Shortly after this conversation, the narrator marries his wife Isabel and goes off to serve in the military. He kind of forgets the promise he made to his mom to watch out for Sonny until after she dies and he gets special leave to attend her funeral. This is when he learns that Sonny wants to leave school, join the army, and eventually play piano for a living.
As hard as he tries, the narrator just doesn't understand his brother. He convinces him to move in with Isabel and her family while he's away in the military, but Sonny eventually runs away, joins the navy, and ends up in Greece.
Once they're both back from war (we're thinking this is the Korean War since it's a little too late to be World War II), they only see each other occasionally. But they always end up arguing about Sonny's decision to quit school and become a musician.
After one particularly nasty argument, the narrator doesn't talk to Sonny for months. When he finally decides to contact Sonny again, he finds him lying on his bed in an apartment surrounded by a ton of other people, many of them musicians. Sonny won't even get up to talk to his brother and they get in another horrible fight. The narrator storms out and Sonny slams the door behind him. The narrator starts to cry.
The story jumps ahead a bit to when the narrator's daughter, Grace, passes away. He recalls how it happened – his wife Isabel is in the kitchen when she hears Grace fall down and then there is silence. When she gets to the living room she sees her daughter writing in pain and then the little girl finally screams a horrible scream. Not long after, she dies from polio and the narrator contacts Sonny the day of Grace's funeral.
The story shifts back to the present when Sonny is living with the narrator. The narrator finds himself alone in the apartment one afternoon and he struggles with whether or not he should search Sonny's room for signs that he's still doing drugs. Before he can decide one way or another, Sonny comes up to the apartment and they finally have it out.
The narrator expresses the anger he's harbored for years. He tells Sonny there's no way to avoid suffering in this world, so he shouldn't think drugs are the answer. Finally, he tells Sonny that all he really cares about is Sonny's well being.
After the argument Sonny invites the narrator to come see him play, and the narrator agrees. They go to a club that night and the narrator sees Sonny in his element. He realizes that he's just Sonny's brother in the club – he's not special when he's in Sonny's world. As he settles in to watch Sonny play, he finally sees what an amazing musician he is. He finally understands a little better what Sonny has been trying to explain to him about music.
As a kind gesture, the narrator sends Sonny a drink, as if to tell him that he finally gets it. As the story concludes, the narrator watches Sonny with a mixture of new understanding, pride, and love.