In August 1949, in the South African village of Ndotsheni ("The Hills of Ixopo"), the black Anglican priest of St. Mark's Church, the Rev. Stephen Kumalo, learns from a letter from his brother (John Kumalo, who lives in Johannesburg) that their sister is in trouble. Stephen decides to travel to Johannesburg to help his sister; he will also seek his son, Absalom, who works in the mines ("Thousands of Miles"). In Johannesburg, Stephen learns that his sister will not leave but she asks him to take care of her young son, Alex.
He finally locates his son Absalom, who had been in jail. Absalom now plans with his friends to steal, so they can get enough money to avoid a life in the gold mines. Absalom's pregnant girlfriend Irina tries to convince him not to take part, but he goes ahead with his plan ("Trouble Man"). During the robbery, Absalom kills Arthur Jarvis, a white friend of his father, Stephen. As Absalom is jailed, Stephen wonders how to tell his wife, Grace, and he realizes he is facing a crisis of faith ("Lost in the Stars").
Stephen knows that his son could either tell a lie and live or tell the truth and die. He prays for guidance ("O Tixo, Tixo, Help Me"). At the trial, Absalom's two friends lie to the court and are freed, but Absalom, truly repentant, tells the truth and is sentenced to hang ("Cry, the Beloved Country"). Stephen performs a wedding between Absalom and Irina in prison and then returns home to Ndotsheni with Irina and Alex. Alex and the child of Arthur Jarvis meet and start to become friends ("Big Mole"). Stephen tells his flock he can no longer be their minister, and their faith is now also shaken ("A Bird of Passage").
On the still-dark morning of the execution, Stephen waits alone for the clock to strike ("Four O'Clock"). Unexpectedly, the father of the murdered man pays him a visit. He tells Stephen that he has realized that they have both lost sons. Out of recognition of their mutual sorrow, and despite their different races, he offers his friendship, and Stephen accepts.