Bitter Fruit is the story of a family trying to come to grips with the past. Living in post-apartheid South Africa, one day Silas Ali comes face-to-face with the man, Du Boise, who raped his wife Lydia nearly twenty years ago. This encounter throws the Ali family into a downward spiral as each member tries to come to terms with what happened.

Under the apartheid regime, Silas worked for in the underground resistance. His secret life put his family into danger and Lydia's rape was probably related to his resistance work. Silas is now working as a liaison between the Truth and Reconciliation Commission (TRC) and the government. Silas remains idealistic and optimistic about the future of the country. His family life; however, is thrown into turmoil when he sees Du Boise. He discovers that his brother-in-law was present the night Lydia was raped. Silas tries to avoid the topic and reality of Lydia's rape, remaining passive as his family slowly breaks apart. Silas attempts to get Lydia to testify in front of the TRC but he is helpless, and unwilling, to take any further actions to help his family because he is caught in his own pain.

For Lydia, the sighting of Du Boise causes memories of the rape to erupt to the surface. She feels again the pain, helplessness, and emotional damage of the rape. In her anguish, Lydia injures herself, giving her a visible symbol of her internal turmoil. She seems to become more emotionally unstable and fragile, as she clings to her son Michael and lashes out at Silas. In the end, Lydia's solution to the pain is to disengage from her family. She takes on a new job, sleeps with a man at her husband's birthday party, watches her son self destruct, and finally, Lydia leaves her town and her husband for a new life elsewhere.

Michael's transformation within the novel is the most drastic. He learns of his mother's rape by reading her diary and he also discovers that he is Du Boise's child. As he struggles to come to terms with this information, Michael embarks on several affairs from which he gains information about Du Boise and a stolen gun from the women he sleeps with. Michael reconnects with the Silas's family, hoping to prove Lydia wrong, and he is drawn into his late grandfather's mosque. In the mosque Michael learns of his grandfather's personal revenge against the man who raped his sister and Michael gains a safe haven for himself. When a young woman he knows admits to him that she has been sleeping with her own father, Michael is pushed to the edge. He kills the woman's father and then Du Boise, before starting his journey to India and safety.