My Son’s Story takes place in South Africa during a time when blacks are fighting to gain full rights of citizenship. The main character, Sonny, is married to a woman named Aila. They have two children, Baby and Will. As the story opens, the two children are young teenagers, and Will witnesses his father leaving the movie theater with a white woman. He believes his father is about to have an affair. Will struggles with this, as it plants the seed for a deep resentment toward his father that continues to grow. He doesn’t want to tell his mother, as he doesn’t want her to be devastated.

During this time, Sonny is a teacher. One day, he leads his students into a demonstration near the school, and he is fired. He becomes swept up in the movement for black liberation and gains popularity as a public political and social activist. The family moves to Jonnesbury, which is a white neighborhood in which they are unwelcome, and this move creates resentment in the family toward Sonny. By this time, Sonny is dedicated to the movement, and he even spends a couple of years in jail due to it. While in jail, he is often visited by Hannah, a woman who continues to give him news about the movement, and they eventually begin an affair.

Sonny realizes he is in love with Hannah but maintains his relationship with his wife, although it is becoming more and more difficult to do so. As he continues carrying on his affair, he becomes cold and distant to his family, which affects each person differently.

It is then revealed that Baby is also involved in the movement, and she moves to Lusaka, Zambia, and becomes pregnant. Aila begins spending more and more time visiting her daughter and grandchild. Sonny sees the effect all of this is having on Will and begins to spend more time at home with him.

A twist in the plot occurs when Aila, who is known to be quiet and uninvolved in the movement, is arrested. The police find evidence in their house related to the movement, which Aila claims she was holding for unknown friends. She is released on bail and becomes a hero among those involved in the movement.

Meanwhile, the woman Sonny is having an affair with takes a better job and is never heard from again. Aila then escapes as a fugitive and lives on her own. Neither Will nor his father knows where she is living. The two of them continue living together, and their relationship changes, as Sonny is no longer having an affair, nor is he involved in the movement anymore. However, Will remains angry with him for his prior actions.