Set in 1950s New York, it continues the saga of the two friends, Reuven Malter, a Modern Orthodox Jew studying to become a rabbi, and Danny Saunders, a genius Hasidic Jew who has broken with his sect's tradition by refusing to take his father's place as rebbe in order to become a psychologist.

The theme of the conflict between traditional and modern Orthodox Judaism that runs throughout The Chosen is expanded here against the backdrop of the changes that have taken place in Reuven and Danny's world in the period of time between the two novels: following World War II, European survivors of the Holocaust have come to America, rebuilding their shattered lives and often making their fiercely traditionalist religious viewpoint felt among their people.

During Talmud class, Reuven and his classmates listen to Rav Kalman's regular tirades about how the modern world is destroying Jewish life.

That fall, Reuven and Rachel agree that they are merely good friends (not romantic partners), and Michael is sent to live in the treatment center that Danny is doing his residency in.

At the same time, word leaks out that there will be a new department in the university that will teach Talmud in a secular manner, which infuriates Rav Kalman.

As the months pass, Michael descends into silent catatonia, which sends panic through Reuven, the Gordon family, and Danny (whose career hinges on the experiment).

Deciding to be true to himself, Reuven uses his father's method of emending the text of the Talmud in order to clarify more complicated passages.

In the end, Rav Kalman gives Reuven smicha, stating that although he vehemently disagrees with his methods, he can hear the love of Jewish text in his voice, something he had not heard since his students were killed in the Holocaust.

He chooses to embrace modernity by using his father's method on the Talmud, and possibly on the Prophets and Writings section of the Bible, but not on the Pentateuch.