Chaim Potok's novel The Chosen is the story of the friendship between the Hasidic Jew Danny Saunders and the more liberal Jewish teenager Reuven Malter in Brooklyn at the end of World War II. At the beginning of the novel, both are fifteen years old and live near one another, although because they go to separate yeshivas (parochial schools) they have never met. The two meet during a softball game between their two schools, in which Danny confronts Reuven and calls him an apikoros (a Jew who denies the basic tenets of his faith) as Danny is on second base. During the baseball game, Reuven pitches to Danny, who hits the ball back at him, hitting him in the eye and shattering his glasses.
Mr. Galanter, Reuven's baseball coach, takes him to Brooklyn Memorial hospital, where he must stay for a week while his eye heals. He stays in the hospital ward with Tony Savo, a professional prizefighter, a young blond boy named Billy, and a small child named Mickey. When Reuven's father, David Malter, arrives, Reuven tells him how Danny intended to hit him and called him an apikoros. However, Danny later visits the hospital; Reuven is bitter and confrontational, and they argue once more, but Danny visits a second time and confesses that he had to win the ball game because of his father. The two begin to discuss the Talmud, and Danny admits that he wants to be a psychologist. They two soon become friends.
After Danny leaves the hospital, David Malter enters and Reuven discusses Danny with him. David tells his son how the Talmud instructs that a person should find a teacher and a friend, and tells Reuven to make Danny Saunders his friend. When Danny visits again, he and Reuven discuss Darwin and Hemingway, and says that he will not like being a rabbi. Reuven is surprised that Danny sounds very little like a Hasid. David Malter finds Danny and Reuven together, and Danny recognizes David, for he has been meeting Danny in the library and recommending books for him to read.
Reuven returns home from the hospital and his father explains to him the history of Hasidism, which began in Poland after the Cossacks led an uprising against the Polish nobility and their Jewish supporters that led to a nearly complete massacre of the Jewish community in Poland. The disaffection after this tragedy led to the formation of Hasidism, with its different sects lead by tzaddikim. Reb Saunders, Danny's father, is a tzaddik and will pass this position on to his son. David Malter then tells how Danny is a great intellect who desires far more than the narrow study of Hasidism, and that the accident has bound Danny and Reuven together.
Reuven meets Danny's father when he visits Danny's home. From the description that Danny gives of Reb Saunders, Reuven assumes that he is a tyrant because he does not allow Danny to associate with outsiders, but Danny insists that his father is not just another human being. During a meal after the Shabbat afternoon service, Reb Saunders gives a speech about the Torah in which he claims that "the world kills us. The world flays our skin from our bodies and throws us to the flames." He refers to gematriya, a numerical frame of reference for the Torah, and afterwards asks Danny if he has anything to say. Danny corrects his father on a point, but Reb reprimands him for only catching the first mistake and not catching the others. Reb then asks Reuven if he liked the gematriya, and Reuven mentions a mistake that had found. There is a sense of relief, as if Reuven has passed a test with Reb Saunders.
Reuven meets Danny in the public library, where he is reading Graetz' History of the Jews, a book that sharply criticizes Hasidism and calls tzaddikim "priests of Baal." Danny takes this as evidence that people are complicated, and discusses psychology and how he is learning German so that he can read Freud in the original text. David Malter tells Reuven that Graetz exaggerates the faults of Hasidism, and there is enough to dislike about Hasidism without exaggerating its faults. Reuven visits Danny, and Reb Saunders asks Reuven to tell him what Danny is reading, for he cannot ask his son. Reuven tells him that Danny is reading psychology, but leaves out that he is studying German so that he can read Freud.
When the school year begins again, Danny and Reuven see each other only on Shabbat, for Reuven's evenings are filled with student council meetings. As the war in Europe ends, news of the Holocaust comes to America. Reuven cannot grasp the news of this tragedy, while Reb Saunders laments "how the world drinks our blood" but thinks that this is God's will. David Malter suffers a heart attack, and while he stays in the hospital Reuven stays with Danny.
Although the Saunders accept Reuven as part of his family, Reuven notices that Reb and Danny speak only when they discuss the Talmud on Shabbat, and during breakfast one morning Reuven makes the mistake of mentioning the possibility of the establishment of Palestine as a secular Jewish state. Reb Saunders becomes enraged, saying that the land of Abraham, Isaac and Jacob will not be built by Jewish goyim while he lives. Later, Danny tells Reuven that Reb was ready to throw Reuven out of the house, and admits that Reb is suffering for the Jews who died in the Holocaust. Danny begins to realize that if he does not take his father's place he won't necessarily break the dynasty, for he has a brother who could take his place. Danny feels intellectually trapped and tells Reuven that he will need him when he tells his father that he will not become a tzaddik.
Reuven and Danny enter Hirsch College, where Danny is miserable because he must study experimental psychology instead of Freudian psychoanalysis. The other students, however, look upon Danny in awe for his abilities, and he is placed in Rav Gershenson's Talmud class, the highest in the school. David Malter becomes quite involved in Zionist activities promoting the idea of Palestine as a Jewish homeland. Danny discusses Freudianism with his professor, Nathan Appleman, and becomes more content when he learns that Appleman respects Freud but not his followers. Because of David Malter's Zionist activities, including a speech in which he declares that the Holocaust will only have meaning when a Jewish state is established, Reb Saunders forbids Danny from having any contact with Reuven Malter.
Danny and Reuven do not speak for the rest of the semester. Reuven grows to hate Reb Saunders for enforcing this separation, and the college becomes more tense because of Zionist activity. Reuven vows to forget Danny, but he is moved into Rav Gershenson's Talmud class with Danny. David Malter suffers a second heart attack. Rav Gershenson rarely calls on Danny, but when he finally does Reuven has prepared extensively for his question and answers well, but using techniques of which Gershenson does not approve.
David Malter returns home once more after his heart attack, and Danny and Reuven begin to communicate through gestures and nods. Zionist agitation at Hirsch College continues, but Reb Saunders' anti-Zionist league essentially dies when a United Nations truce goes into effect and fighting in Israel ceases. Later that year, Danny approaches Reuven and asks him for help with experimental psychology.
Reuven and Danny resume their friendship, and Reuven even visits his home, where he finds Reb Saunders looking haggard and aged. Reb Saunders asks why Reuven never visits on the Shabbat, but does not mention Zionism. Reuven even attends the bar mitzvah for Danny's younger, brother, Levi, who becomes violently ill. Reuven tells his father about Danny's plans to pursue a doctorate in psychology and not become a tzaddik, and David Malter compares Danny to a person waiting to be let out of jail. Danny applies to Harvard, Columbia and Berkeley, and claims that he cannot remain an Orthodox Jew while practicing psychology.
David Malter advises Danny about his plans, and advises him to think carefully about what he will say to his father. Danny realizes that his father must have seen his acceptance letters to graduate school. When Reuven mentions to his father that Reb wondered why he no longer visits on Shabbat, David tells him that this was a veiled invitation to visit him, and advises him to go on Passover.
On the first day of Passover, Reuven visits Reb Saunders, who tells Reuven that he and Danny will go their separate ways and he has known it for a long time. Reb tells Reuven that he may never understand nor forgive him, but he knows how Reuven feels. Reuven realizes that Reb is speaking as much to Danny as he is to him. Reb Saunders tells Reuven how a man is born into the world with only a spark of goodness that is God, and all the rest is a shell that is evil, even if that shell is intellectualism. He mentions the importance of knowing pain to realize how frail and tiny we are compared to God, and says that this explains why he treats Danny the way he does. However, he says that Reuven was sent to Danny by God when Danny was ready to rebel, and he knows that Danny will be a psychologist, but nevertheless will always be a tzaddik. Reb then calls in his son, and asks Danny if he will shave off his beard and earlocks when he leaves. He nods in assent. Reb Saunders breaks into tears, attempting to apologize for his ban on Reuven, then leaves the room. Danny and Reuven both weep for their suffering.
Reb Saunders announces to his followers that Danny will study psychology. Danny prepares to go to Columbia University, and shaves off his beard and earlocks. David Malter asks Danny whether, when he has a son, he will raise him in silence, and Danny says that he will, unless he can find a better way.