Chime begins with the narrator, Briony, speaking about her trial. She informs the reader of her guilt in the matter and that the reader should not be thinking she could possibly be innocent. After this brief introduction the novel returns to the events prior to the trial.

Briony introduces the reader to her father, a clergyman and her sister Rose as well as a new boy, Eldric who would be living with the family at the parsonage. At a funeral the ghosts of dead children began to speak to her, telling her that the Boggy Mun (the spirit of the swamp itself) had sent them the swamp-cough, and that they are asking for her help. They said that the reason for the swamp cough was that the men are planning on draining the swamp, and angering the spirit.

The constable expressed his belief that the witch was Nelly Daws. Briony decided at this point to talk to the Boggy Mun in order to save Rose from the swam cough. Unfortunately, this plan backfired in a massive way, as she found out that the Boggy Mun had given Rose the swamp cough and would not release it from her or another boy in town until the men from London stop draining his swamp. The following day Eldric, Briony and Rose went to the courthouse to testify. Nelly was hanged, but she did not turn to dust. They had hung the wrong woman.

Briony was in the swamp and destroyed a pumping station run by Mr. Clayborne who wanted to drain the swamp. She was nearly caught by Robert, a hired guard, when Eldric arrived and took her aside to discuss the implications of her actions. On her way back from the swamp Briony was attacked by The Hand but saved by Eldric. Briony later asked Eldric about what had happened while she was passed out, and he explained that he had never left her side, missing both the harvest festival and the hayride, as well as lessons with Leanne (much to Briony's pleasure). After this, Eldric invited her to Blackberry Night.

Days later it was Blackberry Night, and Briony had removed her cast. Cecil arrived and tried to force her to kiss him when Eldric came crashing in to save her, hitting Cecil multiple times and dragging him away. Eldric kissed her cheek and then her mouth. There was chemistry between them until Eldric realized what was happening and stopped them. He tried to take Briony home but she ran away before he got to his feet.

While Eldric was talking to Leanne, Mucky Face arrived to attack her but Briony was able to get him to go back to the river, but not before Eldric saw her. She informed him that she had the second sight, the ability to see and talk to the Old Ones. While in the bar she came to the realization that the wave was sent to harm her, and she attempted to figure out who would have sent it. Eldric felt betrayed until she gave him enough implication that he could infer that she was a witch. They discussed his relationship with Leanne, and Briony wrote one of her limericks about it which gave her the spark to realize the truth about Leanne; she was a Dark Muse and had attempted to kill Briony. Briony told Eldric her big secret, that she was a witch.

It was the night of Halloween, and Briony went to the graveyard of the children and called them all to speak about their illness and how the people could stop the swamp cough. They told the people that the Boggy Mun had killed them as a result of the drainage, which sent the crowd into a frenzy. The Stepmother also rose, and informed Briony and all around that not only had she been murdered but she was one of the Old Ones and claimed Briony as her murderer. The crowd turned on Briony, calling her a murderess and calling for her to be hung as a witch. Briony turned to run and the Constable followed, but was shot by Eldric. Briony ran into the swamp where she then saved Eldric from The Dead Hand, helped him up and they walked back to the village, to take him to Dr. Rannigan.

There is a time lapse, and it is now the last day of the trial, the courtroom is almost completely full. Eldric interrupts and says he has information that could help, turning her words into a story, much like she did with Leanne. He suggests that Stepmother was a dark muse. Father then enters the conversation revealing that she was a Dark Muse. Rose then enters, saying that she is ready to reveal her secret, having been persuaded by Robert. She reveals that Stepmother had taken the register of the midwife, which read that Briony had been born between November 1st and Second, making her a Chime Child, not a witch.

It is another time lapse, it is now March. Eldric and Briony are in good shape, and she is even talking to Father again. Briony sneaks out of the house to the swamp where she talks with the Reed Spirits and promises to write down their stories. She is to apprentice with the Chime Child when she recovers from the injuries she sustained saving Eldric. A motorcar arrives and Eldric exits and sits by her. They discuss his lost hand, and he expresses his lack of masculinity and attempts to unbutton Briony's blouse to which she responds negatively. Eldric backs off and tells her again about his love for her to which she responds with an outpouring of emotion about her love for him. This time when he says he loves her, she believes it, she believes that she is someone who can be loved.