In 1944 Brooklyn, fifteen-year-old Reuven Malter prepares to play a baseball game: his own Modern Orthodox school against a team from an ultra-orthodox Hasidic yeshiva. It becomes apparent that the only good player on the opposing team is Danny Saunders, the son of a nearby Hasidic Rabbi. The game becomes something of a war between the two teams, seemingly symbolic of their differing ideologies. In the last inning, with Reuven's team in the lead, Reuven is put in as pitcher. When Danny gets up to the plate, he hits a line drive straight at Reuven's head, which breaks his glasses and drives a small piece of glass into his eye. Reuven's team loses and Reuven is rushed to the hospital.
Danny comes to the hospital in an attempt to apologize, but Reuven is still livid at Danny and rejects his attempts, which angers Reuven's father, who reminds Reuven it is important to listen to someone who asks to be heard. When Danny returns the next day, Reuven forgives him and they quickly become friends.
Reuven learns that Danny possesses a photographic memory, enabling him to study an astonishing amount of Talmud per day (set by his father), yet still leaving him time to pursue other subjects. Danny tells Reuven that he goes to the library to read books on science and literature, and that a man at the library has been recommending books for him to read. Danny knows that he is expected to someday take over his father's position as the rabbi for his community, but wishes he did not have to and that instead, he could pursue psychology. Reuven would like to become a rabbi, though his father would like him to pursue academia. Reuven learns that his father, a teacher of Talmud, is the man who has been recommending books to Danny at the library.
When Reuven is released from the hospital, his father discusses the history of Hasidism with him. He then explains that only once in a generation a mind like Danny's is born, and that Danny cannot help his need for knowledge, but that Danny is also a lonely boy who needs a friend.
The next day, Reuven goes to Danny's family synagogue where he witnesses a discussion between Danny and his father which spans over the entire Talmud. After the Sabbath has ended, Danny reveals to Reuven that his father only speaks to him when they study Talmud together. The two boys also discover that they will be attending the same university, much to Reuven's delight. That Sunday, Danny, and Reuven meet at the library, where Danny reveals his fascination with the human mind and his desire to study the works of Sigmund Freud, for which he is teaching himself German.
The next week, Reuven goes to the Saunders house again to study Talmud with Danny and his father. When Danny leaves the room to prepare tea, Rebbe Saunders reveals to Reuven that he knows about Danny's visits to the library and wants to know what Danny is reading. He adds that he knows he cannot prevent Danny from pursuing knowledge, but that he fears his son will lose his Orthodox faith. Reuven immediately tells Danny about the talk, and later, Reuven's father discerns that Reb Saunders used his conversation with Reuven to communicate with Danny indirectly.
The coming year is dominated by the Allied victory in World War Two, and the death of Franklin Roosevelt, which brings grief to the Malters. In addition, news of the Holocaust reaches American soil, which sends all the characters, especially Rabbi Saunders, into a state of depression. During the summer of that year, Reuven's father suffers a heart attack, and Reuven goes to stay in the Saunders home. At one meal, Reuven mentions that some feel it is time to establish a Jewish state, which sends Rabbi Saunders into a fierce tirade against Zionism; for the ultra-orthodox, a secular Jewish state established by man without the coming of the Messiah is against God's will.
The next year Danny and Reuven enter college at the Samson Raphael Hirsch College and Seminary. Danny is miserable because the psychology department at the university is only experimental psychology and not analytical. Eventually, Danny's psychology professor tells him that he should go into clinical psychology.
Later in the year, Reuven's father gives a speech at a Zionist rally, which is covered by the Orthodox press, and leads Rabbi Saunders to forbid Danny to have any contact with Reuven. Reuven does not cope well without his best friend and his grades begin to suffer. Soon afterward Reuven's father has a second heart attack followed by a lengthy hospitalization. Reuven copes with his father's absence by studying the Talmud with greater intensity, eventually mastering a very complicated section of the Talmud.
After two years, just as the violence in Palestine comes to an end (the 1948-49 Arab-Israeli war) and Reuven's father has recovered from his heart attack, Danny is allowed to resume his friendship with Reuven because the Jewish state is now a fact, and no longer a point of dissension.
As the years pass, Danny's father continues to remain silent with Danny. Danny reveals to Reuven that he will not take his father's place. Instead, he will apply to graduate school and pursue a doctorate in clinical psychology, and his younger brother, Levi, will assume the tzaddikate. Danny applies to Harvard, Columbia, and Berkeley. He is accepted into all three universities, but cannot understand why his father does not speak to him about it, because the acceptance letters came by mail and were surely seen.
On the first day of Passover in Danny and Reuven's senior year of college, Reb Saunders invites Reuven to their home to talk with him and Danny. Reb Saunders tells Reuven that he knows that Danny will not be assuming the rabbinate, that he has known for a long time, and he accepts it. He then explains why he raised Danny in silence: he feared that Danny's phenomenal intelligence would lead him to lack compassion for others. Therefore, he raised Danny in silence so that he could learn what it is to suffer, and therefore, have a soul. He also relates Danny to his older brother, who ran away from his homeland in Russia and became a secular professor and died in Auschwitz.
Reb Saunders expresses his gratitude to Reuven and his father for helping Danny at the point where he was ready to rebel, to help Danny remain a part of the Orthodox Jewish tradition, even if he cannot assume the rabbi role. To his father's questions, Danny indicates that he will remove some of the visible indicators of Hasidism (his full beard and earlocks) but will remain an observer of the commandments. Reb Saunders says that Passover is the holiday of freedom and that he must let Danny be free.
That September, on his way to graduate school at Columbia, Danny comes for a brief visit without his beard and earlocks. He says that he and his father now talk.