The Chosen is set in the mid-Twentieth Century, in Williamsburg, Brooklyn, New York City. The story takes place over a period of six years, beginning in 1944 when the protagonists are fifteen years old. It is set against the backdrop of the historical events of the time: the death of President Roosevelt, the end of World War II, the revelation of the Holocaust in Europe, and the struggle for the creation of the state of Israel.
Reuven and Danny meet for the first time as rivals in a softball game between their school teams. The game turns into a spiritual war between Danny's Hasidic and Reuven's Modern Orthodox yeshivas. Danny's batting style is such that the ball is sent speeding back up the middle of the field, and so he receives a reputation of trying to kill pitchers. Angered by unsuccessful attempts to hit Reuven's previous pitches, Danny hits a line drive toward Reuven, shattering his glasses and sending him to the hospital with an injured eye. While Reuven is recovering from his injuries, Danny visits him and apologizes; and the two become best friends over time, despite the difference in their upbringings. Reuven learns that Danny's father, a respected Rebbe, only talks to Danny during religious conversations - Danny is being brought up 'in silence'. Reuven also learns Danny's deepest secret: he wishes to become a psychologist rather than inherit the position as tzaddik as his father wants. The only people who know about this are Reuven, and a man who has been recommending books for Danny to read and later discussing them with him, who is later revealed to be Reuven's father.
Reuven comes to experience the pain of silence himself while the two young men are in college together. Though accepted as family after he stays with the Saunderses while his father is in the hospital, Reuven incurs Reb Saunders's wrath when he speaks favorably of the struggle to establish a secular Jewish nation in Palestine, which Saunders vehemently opposes. When Mr. Malter makes a speech at a pro-Israel rally that makes the newspapers, Saunders forbids his son to speak to Reuven, or even mention his name. (Danny breaks this order once, to let Reuven know, but tells him, "I won't go against my father. I won't!") The ban lasts for two years, during which time Reuven experiences anguish, rage, and depression (particularly after his father suffers a heart attack), before learning to cope with being alone.
Their friendship resumes after modern Israel is founded; Danny explains to Reuven that Reb Saunders has relented, since the new nation is "no longer an issue; it's a fact." Reuven finds that Danny has come to terms with the silence imposed by his father, having discovered that silence can be a teacher, and a source of beauty as well as pain. Danny himself waits in fear for the day following graduation, when he must tell his father that he does not wish to succeed him. (Reb Saunders already knows this to be true, after Danny receives an acceptance letter from Columbia University.)
Father and son reconciled
Reuven again finds himself a buffer between father and son when, in the novel's climax, the two friends learn Reb Saunders's purpose for raising his son in silence: Reb Saunders had discovered early on that his son's dawning intelligence was far outstripping his sense of compassion for others. He wanted his son to understand the meaning of pain, so he shut him out emotionally. Finding the grown-up Danny indeed has a heart, and cares deeply about other people, Reb Saunders is willing to give his blessing to Danny's dream of studying psychology. "He will be a tzadik for the world," Reb Saunders tells Reuven. At last Reb Saunders breaks his silence and truly talks to Danny, asking Danny to forgive him for the pain he caused, bringing him up as he did. The words finally spoken, Reb Saunders leaves the room, and both boys burst into tears.
Danny visits Reuven on his way to Columbia University, his Hasidic side locks shorn and his clothing up to date. Reuven has definitely decided he wants to be a rabbi, and is going on to study at a yeshiva. Danny tells Reuven that his younger brother Levi will take his place as his father's successor, and his own relationship with Reb Saunders has completely changed. "We talk now," he says quietly. Danny is finally set free, and Reuven and Danny taste profoundly the pain in life, and the consolation of deep friendship. Danny goes on to study psychology.
Danny's phenomenal mind compels him to seek knowledge other than that permitted by his father, and he spends his spare time reading voraciously in secret in the public library. (Danny tells Reuven about an older man he met there who has been recommending books for him to read; both are astonished when the man turns out to be Reuven's own father.) Danny does not want to inherit his father's position as leader of their sect, as is expected of him; he desires instead to become a psychologist. He learns to read German just to read a book by Freud. Another great conflict in his life is that his father does not speak to him, except when they study Jewish law together; this has been so since he was about ten, when his father told him not to come to him about problems anymore.
Reb Saunders welcomes Reuven as his son's friend, even though he disapproves of his father's work. "You think it is easy to be a friend?" Reb Saunders says to Reuven when they first meet. "If you are truly his friend, you will learn otherwise." Reuven does learn as he is put in the position of being a buffer between father and son. Reb Saunders forces Reuven into a position to tell him of his son's secular studies even though Reb Saunders had known about it for a while already. Reuven impresses Reb Saunders by his understanding of Jewish law and tradition. Reb Saunders impresses Reuven in turn, as Reuven sees the important role he plays to the people of his congregation. He raised his son in silence, which allowed him to learn to find his soul. He was a very difficult man to understand, but a great leader.