Now middle-aged, two cousins reunite at their ancestral country house in the small town of Blémont in Normandy, France. The house itself contains brutal secrets from the time of the Second World War, when Thérèse's and Léonie's mothers were young women. Thérèse, who has been living a sheltered life as a nun, returns to the Martin estate, where Léonie waits for her. Léonie, having chosen a life with Baptiste, the son of a local farming family, has been living in the Martin house and raising a family. Léonie is full of intense anticipation and anger as she waits for Thérèse to arrive. As young girls, the two women shared the role of "daughter of the house" when Léonie and her mother came to spend summers in France. The two cousins have a relationship full of shared secrets, jealousies, and competition within the household, colored by Baptiste's presence, secrets from the past, sexual exploration, and Antoinette's progressively deteriorating health.

The novel is a retelling, from two mixed viewpoints, of the girls' childhood and particularly the "odd summer" when the two reach adolescence and Antoinette dies of cancer. The girls watch as Antoinette becomes weaker and then dies, and they deal with the pain of her loss in their own ways. Léonie builds up a fierce anger against the other girl as Thérèse tries at all costs to win the attentions of her father, Louis. Thérèse becomes more and more convinced that her own pain and sacrifices will aid her mother's journey through purgatory and into the afterlife. When Antoinette dies, Louis suffers a stroke, and Antoinette's widowed sister Madeleine care for him. When it becomes clear that Madeleine will take Antoinette's place as Louis' partner, meaning that Léonie will now be his daughter also, Thérèse decides to join the convent and retreat to a life in the service of God.

When Thérèse returns to Blémont as an adult, it becomes clear that many secrets and tensions have never been resolved between the two women, including personal secrets and the larger mystery of the horrors and transgressions that took place in and near the Martin estate during the war years just before the two girls were born.

Earlier in Thérèse and Léonie's childhoods, the girls' maid and guardian Victorine, a local woman who proudly abides by many of the old traditions, shows them a place in the woods behind the house where an ancient shrine has stood. The place is shrouded in mystery because ancient pagan traditions are still celebrated here at harvest time. These celebrations are melded with the Catholic worship of the Virgin Mary at the shrine. During the war the original shrine was dismantled. The woods also harbor a darker secret, one that the entire village prefers to forget.

Three mysteries are central to the novel. The first is the mystery of the transgression that took place in the cellar and involves Antoinette. The second involves the back stairs of the Martin house and the back bedroom where Léonie sleeps. This mystery is tied to the images Léonie sees in her nightmares. The third mystery is that of the mystic vision that both girls claim to have seen. It is only at the very end of the novel that Léonie, after persistently questioning of the adult characters, finally learns the village secret from Rose. During the Nazi occupation of the village a Jewish family was found hiding in the Taillés' barn. The family was then transferred to the back bedroom of the Martin house, along with Henri Taillé. The next morning the local man, along with the young family, was taken to the nearby woods and shot.

Throughout the novel the author builds on the secrets that Léonie and Thérèse share. These secrets lurk within the house, surfacing in Léonie's intense nightmares. The girls are told only that Antoinette suffered horribly during the war and that the cellar and the back room where Léonie sleeps harbor the house's secrets. By the end of the novel it is clear that one secret being kept from the girls is that Antoinette was sexually assaulted during the war, though the name of her aggressor continues to be a mystery. Whether the perpetrator was a German soldier billeted at the house or Louis himself, Antoinette's ensuing pregnancy necessitated her marriage to Louis and forced her to give up her dream of becoming a nun.

During her childhood, Léonie is prone to nightmares brought about by voices crying out and chanting around her in the back bedroom where she sleeps. At the end of the novel, Rose finally tells Léonie that this back room is where the young Jewish family and Rose's husband Henri spent their last night. The Nazis killed Henri, who harbored the fleeing family, as a lesson for others in the village. Rose also tells Léonie that she had been pregnant at the time and that the death of her husband brought about early labor and a stillbirth. This partially explains why Thérèse spent the first few years of her life with Rose and not with her mother Antoinette. Rose was paid to be Thérèse's caregiver until a husband could be found.

Thérèse and Léonie have reached early adolescence in the summer that Antoinette dies. The two girls have outgrown the sexual and religiously tinted games they shared previously, and their relationship deteriorates to one filled with competition and jealousy. The girls compete for the affection of the adults in the household. Léonie struggles with being excluded and snubbed because of her Englishness, although she is only half English, and Thérèse takes every available opportunity to comment on any idiosyncrasy that Léonie exhibits.

Like their mothers, who as sisters both inherited the Martin estate, Thérèse and Léonie compete for the position of daughter of the house. The girls compete for the affections of Louis, Antoinette's husband, soon to be a widower, and of Baptiste, a local farmboy whose eventual marriage to Léonie is a transgression of the social differences that were so important at the time. Like Louis, who married into the family to cover up Antoinette's shameful pregnancy, Baptiste crosses a social barrier by marrying Léonie and becoming part of the Martin family.

The summer that Antoinette dies, Léonie goes to the woods and sees a vision of an olive-skinned woman dressed in red and gold. Not to be outdone, Thérèse claims that she also sees a vision of the Virgin Mary. Thérèse's version conforms to people's expectations because she describes a white woman dressed in blue and carrying a veil. Though Madeleine believes that Thérèse's vision is suspiciously similar to the statue in her niece's room, the villagers believe in the vision and worship at the shrine. The village priest le Curé attempts to put Thérèse in her place and dispute the vision, but the bishop comes to visit and a chapel is eventually constructed at the site.

Later that summer, after Antoinette's death, Thérèse receives a box of letters that Antoinette had written to her sister, Soeur Dosithée. The letters imply that Antoinette was sexually assaulted in the cellar. The letters do not say that Antoinette likely was attempting to hide the statue of the Virgin Mary before it was destroyed when the shrine in the woods was dismantled. Thérèse, her identity being thrown into question and suffering from the loss of her mother, claims that she and Léonie are sisters. She permits Léonie to read only one carefully chosen letter, then tells Léonie about Antoinette's rape by a German soldier. Thérèse throws the letters into the range, where they go up in flames along with any truths they contain.

Léonie kisses Baptiste in the woods after a pagan celebration in the clearing to get back at Thérèse for taking away her sense of security and identity, as she is now unsure whether her father was a German or Louis. At the celebration, there is dancing and the innuendo of further sexual activities that will begin when the young people leave. After Thérèse has stolen Léonie's vision and made Léonie question her own identity, Léonie makes love to Baptiste, knowing that Thérèse is watching and that Thérèse also fancies Baptiste.

Thérèse, meanwhile, feels that Madeleine and Louis will likely become partners now that Antoinette has died. Thérèse feels rejected, as she has been very close to her father, doting on him and relishing his attention. Louis, who has suffered a stroke, is unable to respond when Thérèse announces at a luncheon for the bishop that she will pursue a life of religious contemplation and become a nun when she turns sixteen.

At the conclusion of the novel, Thérèse and Léonie reunite after decades of silence and separation. Louis did remarry, but he and Madeleine have been dead for several years. Léonie married Baptiste, and the two have brought up their family at the Martin estate. Thérèse has returned from the convent with a journal about the years surrounding her mother's death. Thérèse and Léonie stay up talking well into the night about that time in their lives. Thérèse wants to put things straight about her vision and perhaps recant it.

Thérèse also is interested in the Jewish history of the area, and it is possible that she has come back to tell the truth about the bones that were found under the shrine. An enquiry is opening, and racist graffiti recently has been found on Henri's grave. These bones, belonging to Henri Taillé and the family he was murdered with, were hidden by the Nazis under the stones at the shrine and then given a quick and private burial in the graveyard by le Curé when they were found years later as the shrine was being reconstructed.

In the morning, Thérèse visits the church, which has been decked out in preparation for the harvest festival. Every year the villagers celebrate the harvest festival and their devotion to the Virgin Mary by taking her statue on parade. Thérèse must realize that much of this celebration is based on pretence, as she made up the story of seeing the Virgin Mary. Her retreat to the convent was a way of hiding the pain of her mother's death and Louis' remarriage to her aunt Madeleine. This series of events robbed Thérèse of her role as favorite and gave Léonie equal rights as daughter of the house. Impulsively, Thérèse takes Léonie's cigarette lighter and sets fire to the church.

In one of the final scenes in the novel, Thérèse calls out for her mother and runs toward the door of the church, rushing to outrun the flames that surround her. Léonie decides to finally go public with the secret that she has been carrying for many years. In the nightmares of Léonie's childhood, the names of the murdered family members were revealed to her. In these dreams she also heard the name of the informer who led Henri and the young family to their deaths.