Reuven Malter, the narrator, starts The Chosen by describing his native Williamsburg: a neighborhood of Orthodox and Hasidic Jews, who almost never mix or interact. After establishing the setting, the action begins with a softball game. Reuven’s team is playing a Hasidic team on which Danny Saunders is a key player. During a rough game, Danny ends up hitting a softball directly into Reuven’s eye, causing his glasses to shatter, and sending him to Brooklyn Memorial Hospital. After a surgery Reuven seems to be healing well but there is a chance that he will be blind in one eye.
Danny comes to the hospital to apologize and Reuven refuses to speak with him. Finally, with Mr. Malter’s urging, Danny and Reuven do speak and feel a great connection to each other. Reuven’s eye heals well and Danny and Reuven become best friends.
The rest of the novel depicts Reuven and Danny’s navigation of adolescent life, but they do not have the typical concerns of teenage boys. They are growing up during WWII in different but both very religious Jewish communities and most of their time is spent discussing academics, religion, Jewish culture and tradition as shown by their nearly constant study of the Talmud. Danny’s father, Reb Saunders, is the tzaddic (religious leader) of his Hasidic community and Danny is supposed to eventually take his place. This position has been passed down through his family for generations but Danny does not want to become a rabbi. He wants to be a psychologist. On top of this, Reb Saunders believes in bringing up his son in complete silence, so Danny feels utterly alone, and truly needs his friendship with Reuven. Reuven and his father help Danny through his difficult choice to break with tradition and possibly form a life outside of the only culture he knows.
Reuven and Danny go to Hirsch College together and Danny delves even deeper into psychology as his major. Then disaster strikes for Reuven and Danny’s friendship when Reb Saunders forbids his son to speak with Reuven because of Danny's father's Zionist activities. Danny's father has been working to support the creation of a Jewish state in Israel as a response to the horrors of the Holocaust. He believes that it is the responsibility of American Jews to maintain the Jewish faith after such destruction. Reb Saunders believes that this is blasphemous; he disagrees with the idea of a secular Jewish state. In Reb Saunders’ mind a Jewish home in Israel should only exist after the coming of the Messiah. He believes that Jews must accept the horrors that have happened as God’s will and continue to wait for the Messiah. These radically different religious responses to Jewish suffering break apart Reuven and Danny’s friendship for two years.
When Israel becomes a reality, and more Jews (including a Hirsch College alum) are dying to defend the state, Reb Saunders finally gives in. Danny and Reuven begin speaking again but Reuven now hates Reb Saunders. Reb Saunders keeps asking to see Reuven, but Reuven continues to make excuses. Finally Mr. Malter tells his son that Reb Saunders clearly wants to tell him something and that he should never refuse to listen to another person. Reuven agrees to go to the Saunders home. Reb Saunders tells Reuven, while Danny is still in the room, that he knows that Danny wants to become a psychologist. He goes on to explain why he used silence to bring up his son: he saw from an early age that his son was brilliant, but also saw that he had no soul. He wanted to teach Danny about suffering and pain through silence. Reb Saunders says that even if his son would not become a tzaddic, he wants him to have the soul of a tzaddic. Reb Saunders then speaks to his son about something other than the Talmud for the first time since he was a small child. Danny promises to keep the Ten Commandments and soon after Reb Saunders shares the news that Danny will not be following him as tzaddic with his congregation. They eventually are able accept that Danny’s little brother Levi will become the next tzaddic. Danny goes to Columbia to study psychology and says goodbye to Danny and Mr. Malter, promising to come see them soon.