The novel opens with Rahel’s return to Ayemenem after learning that her twin brother, Estha, has returned home after several years. They are both thirty-one years old and have not seen each other since they were children when Estha was sent away to live with his father, Babu. The year is 1993. The narrative then moves back in time, as it does several times in the novel, to 1969, when seven-year-old Rahel and Estha are at the funeral of Sophie Mol, their nine-year-old cousin. At the funeral, Rahel imagines that the painter of the cathedral’s ceiling has fallen to the floor and his head is spilling blood out “like a secret.” She also imagines that Sophie Mol is alive and calling out as she’s being lowered into the earth in her coffin. On the train ride back to Ayemenem after the funeral, Rahel and Estha’s mother, Ammu, is in a trance muttering the words “He’s dead . . . I’ve killed him.” Rahel and Estha don’t know why she says this. 

The narrative switches back to the present, as Rahel looks out over her family’s former pickle factory, Paradise Pickles & Preserves. The factory was started by her grandmother, Mammachi, who had a prized banana jam recipe. Next, the narrative goes back in time to the day the family goes to pick Sophie Mol up at the airport. On the way, they encounter a communist rally and Rahel thinks she sees Velutha, a worker at the family’s pickle factory and someone whom they employ in their home as a servant. Baby Kochamma, Rahel’s grandaunt, is embarrassed when one of the marchers forces her to say a Communist slogan. 

The story continues to circle back and forth between the past and present. In the next scene, readers see the family at the theater the night before Sophie Mol’s arrival. Estha is too loud inside the theater and is sent to wait in the lobby as the rest of the family watches the movie. While alone, a concession stand worker sexually assaults Estha. Rahel, sensing something is wrong, snaps at her mother, causing her mother to say that when you hurt people, “they love you a little less.” This comment sends Rahel reeling and makes her anxious that she could lose her mother’s love at any moment. 

In the present, Rahel runs into Comrade Pillai, a Communist leader at a temple. He congratulates her on still involving herself in India’s traditions and shows her pictures of when she and his son were playmates as children. One of the pictures has Sophie Mol in it, which reminds Rahel of the day they picked her up at the airport. That day, the family was doing their best to impress Sophie Mol, while Rahel was scolded and made to feel bad for getting her dress dirty. 

The narrative turns to Ammu’s death. She dies while out of town on a job interview, alone in a room. She is thirty-one, the same age Rahel is when she returns home to Ayemenem. A young Rahel watches as her body is pushed into the crematorium oven. She doesn’t write to Estha to tell him since they share a psychic bond and, to her, it would be like writing a letter to a part of her body. It is in this moment that one of the narrative’s refrains, “Things can change in a day,” occurs.

At Sophie Mol’s welcoming party, a cake is served and the family sings songs to her. Ammu catches sight of Velutha for the first time as a “man,” and he catches her looking at him. They meet later and begin a secret affair. Back at the pickle factory, the kids decide to go to the History House, an old hut where the Paravans, or Untouchables, live. They find Velutha’s paralyzed brother inside, who tells them how to fix the boat they find. Back home, their mother Ammu dreams of making love to a one-armed man and almost drowning with him in the sea. The story jumps back into the present, as the twins meet outside the temple to watch a Kathakali dance about violence and retribution. The story shifts to focus on Ammu’s brother Chacko and the relationship he has with his ex-wife, Margaret Kochamma, who are parents to Sophie Mol. Shortly after Sophie Mol is born, Margaret leaves Chacko for another man, Joe. When things don’t work out with Joe, Margaret becomes desperate to return to India, and to bring Sophie Mol with her.

Velutha’s father, Vellya Paapen, comes to Mammachi’s door one day and reveals that Velutha and her daughter, Ammu, are having an affair. Mammachi, furious, kicks him out. Baby Kochamma, trying to protect the family name, but also sensing an opportunity to get back at Velutha for her embarrassment with the Communists earlier, decides to go to the police station to report the affair and to make claims against Velutha’s character, claiming he raped Ammu. Mammachi summons Velutha to the house and tells him he’s banished from the family and the factory. Stunned, Velutha goes to Comrade Pillai’s house for protection, but he is denied.

The story turns to the events surrounding Sophie Mol’s death. Seven-year-old Rahel and Estha decide to take a boat to go to the History House after their mother scolds them, and they invite Sophie Mol along. Their boat capsizes when it hits a log and Sophie Mol drowns. This event occurs on the same day Velutha is banished from Mammachi’s home. The twins fall asleep on the veranda of the History House after looking for Sophie Mol all night, not realizing that Velutha is sleeping inside. The police find Velutha inside and beat him nearly to death over Baby Kochamma’s claims, while the twins overhear the whole thing. Later, when the police chief finds out that Velutha is actually innocent and did not rape Ammu, he tells Baby Kochamma that Rahel and Estha must testify that Velutha kidnapped them or she’ll be charged with making a false claim. Baby Kochamma convinces Rahel and Estha that they “murdered” Sophie Mol and that their mother will go to jail with them if they don’t testify against Velutha. She chooses Estha to testify against Velutha, which he does as he looks over Velutha’s dying body in the police station. 

Back in the present, Estha and Rahel meet in Ammu’s former bedroom. They make love, an act not so much of passion, but of “hideous grief” between them. The narrative turns to Ammu and Velutha’s affair and the sweet moments, the “Small Things,” they shared on the riverbank. Each night as Ammu and Velutha parted, they would say, “Tomorrow? Tomorrow” to each other. On the last night they meet, just before Velutha’s death, Ammu turns back one more time to say “Tomorrow.”