The book opens in 1977. Lydia Lee is dead, but all her family knows is that she hasn’t come down to breakfast. Lydia’s mother Marilyn goes up to her room to look for her, and finds everything in its place but no sign of Lydia. Lydia’s siblings Nath and Hannah leave for school, while Marilyn begins to fear that something terrible may have happened. Meanwhile, Marilyn’s husband James is at his office in Middlewood College, unaware that anything is wrong. James is a tenured professor of American History; one of his graduate student teaching assistants, Louisa Chen, knocks on his door and the two discuss their students’ work. Their conversation is interrupted by Stanley Hewitt, who James finds irritating. Then Marilyn calls and asks James to come home.
Back at the house, police officers tell Lydia’s family that teenagers often run away because they are angry with their parents, and that most come home within 24 hours. Officer Fiske asks about an incident in which Marilyn went missing 11 years before, but James quickly dismisses this as a “miscommunication.” After the police leave, James and Marilyn write down a list of Lydia’s friends. Nath says nothing, but knows that the girls on the list are not actually close to Lydia; she doesn’t have any friends except the Lee’s neighbor, Jack Wolff, whom Nath strongly dislikes. However, even as James and Marilyn call all the girls they believe to be Lydia’s friends, Nath doesn’t mention Jack. Meanwhile, Hannah keeps quiet about the fact that at 2am the previous night, she’d seen Lydia walk across the front lawn away from the house. The next day, a passerby notices that there is a rowboat floating in the middle of the lake at the end of the Lee’s street. The police ask James if Lydia can swim and he tells them she can’t; a day later, Lydia’s body is found in the water.
The narrative jumps back to 1955, during Marilyn’s first year at Radcliffe, the women’s college within Harvard University. Marilyn is an excellent student who dreams of becoming a doctor, but faces sexist opposition from both her male peers and professors. Marilyn’s mother Doris Walker is a highly traditional woman, a home economics teacher who has never left her hometown in Virginia. In Marilyn’s sophomore year, she enrolls in a new course called “The Cowboy in American Culture.” She is entranced by the instructor, James, a graduate student in the history department and the first “Oriental” (Asian-American) person Marilyn has ever seen. After the first lecture, Marilyn goes to James’ office hours and kisses him. The two quickly form a relationship. James was born in California to Chinese immigrants who worked in the cafeteria of Lloyd Academy, a small boarding school that James attended after passing the entrance exam at six years old. James goes on to attend Harvard for both his undergraduate and graduate degrees, yet he never feels like he fits into American society. During the spring after meeting James, Marilyn discovers that she is pregnant, and the two marry quickly. At the wedding, Doris tells Marilyn that “it’s not right” for her to marry James, and Marilyn never speaks to her mother again.
Back in 1977, the Lees attend Lydia’s funeral. After the service, Nath aggressively questions Jack and is scolded by James for behaving inappropriately. The narrator mentions that Jack’s mother, Janet, leaves Jack unsupervised during her shifts working as a doctor at the hospital, and that Jack has a reputation for taking the virginity of girls at his school. Later that day, Nath notices that the police are questioning Jack and Janet and he spies on the conversation. Jack tells the police that Lydia was always sad, and that this was due to her poor grades, her parents, and the fact that Nath is about to leave home to attend Harvard. Meanwhile, James has gone to his office to read Lydia’s autopsy report. While there, Louisa knocks on his office door. Seeing that James is visibly shaken, she offers to cook him lunch at her apartment. They go back and immediately sleep together, after which James sleep soundly for the first time since Lydia’s death.
The narrative rewinds 11 years in time, when Lydia is five years old and Hannah is not yet born. At the Middlewood Christmas party, Marilyn asks a professor of chemistry, Tom Lawson, if he would consider hiring her as a research assistant. He tells her he’d be happy to consider it as long as James doesn’t mind. That spring, Marilyn learns that Doris has died. She drives to Virginia to pack up her mother’s belongings, and finds no trace of Doris in her house other than her beloved Betty Crocker cookbook, which Marilyn takes home with her. The cookbook contains recipes and instructions on “keeping” a happy, harmonious household; its advice includes that wives should make eggs in their husband’s preferred style. Meanwhile, James takes Nath to swim at the Y, but Nath is humiliated by the other kids ganging up and shouting racist insults at him. Shaken by her confrontation with the reality of Doris’ life, Marilyn concocts a plan to leave her family, finish her undergraduate degree at a community college in Toledo, and finally pursue her dream of attending medical school. She writes a note explaining her decision to leave to James, but she tears it up and departs without leaving a note. Her family is stunned by her sudden disappearance.
As time passes after Lydia’s death, the police and news coverage both emphasize that she was lonely; most articles claim that her death was likely a suicide. Marilyn insists that this is not true, that Lydia was “very happy” and “loved school.” She and James fight, with Marilyn accusing James of being overly deferential to the police. Meanwhile, Nath and Hannah walk to the lake. Nath sees Jack and is overcome by a desire to punch him, but Hannah stops him. Nath explains that he is convinced that Jack was involved with Lydia’s death, and he adds that Lydia fell in the lake years before, when Hannah was not yet born.
The narrative returns to the summer in which Marilyn disappeared. James enlists the help of the police in finding her, but he had secretly already discovered the torn-up pieces of her note and thus he knows she left voluntarily. Life in the Lee household has quickly fallen apart; James fails to make adequate meals for the children, the family rarely leaves the house, and all three of them spend most of their time aimlessly waiting for Marilyn to return. Nath manages to distract himself with a newfound interest in outer space, and he watches the news coverage of the launch of the Gemini 9 space flight with glee. When he tries to tell James about it, however, James slaps him. In Toledo, Marilyn devotes herself to her studies, quickly regaining her previous prowess at scientific work. However, she desperately misses her family, and calls them every day without saying anything. One day, after a series of dizzy spells, Marilyn faints and goes to the hospital, where she discovers she is pregnant. A nurse calls James, and Marilyn decides that she must return home and give up on her medical ambitions forever. Back in Middlewood, Lydia tells Marilyn that she “lost” the Betty Crocker cookbook, when in fact she hid it because she knew it made her mother sad. Marilyn takes this as a sign that Lydia is rejecting traditional gender roles and she vows to encourage her daughter to study science and become a doctor herself. Meanwhile, Lydia vows to do everything her mother asks in order to prevent her from leaving again. A few days later, Nath and Lydia go to the lake, and Nath is overcome by a sudden sense of frustration with his parents’ favoritism of Lydia. He pushes her into the lake, where she nearly drowns before Nath helps her back to shore. They do not tell their parents about what happened.
Ten years pass, during which time the world is shaken by dramatic political events and shifting social norms, including the gains of the women’s liberation movement. James and Marilyn are still fixated on Lydia, with James encouraging her to attend social events and have lots of friends, and Marilyn enrolling her in college-level science classes. Marilyn boasts that Lydia is a “genius,” unaware that she is failing physics and only barely passing biology. Meanwhile, when Lydia discovers a letter from Harvard informing Nath that he has been admitted to the class of 1981, she hides it in a desperate attempt to force Nath to stay in Middlewood. Eventually, however, another letter arrives and Nath finally discovers that he got in. The family’s celebration is interrupted by Lydia suddenly exclaiming that she is failing physics, which infuriates Nath. At Christmas, James gives Lydia three self-help books with advice on how to make friends; while Lydia pretends to be happy, in reality she is crushed by this gift. At school, Lydia decides to befriend Jack, who is dubious of her sudden desire to smoke and her claim that she doesn’t care about physics. Jack asks Lydia what it’s like to be the only non-white girl in school, and Lydia explains that it means everyone assumes they know something about her before they’ve met her.
The narrative jumps forward to show the Lees continuing to struggle in the wake of Lydia’s death. James and Marilyn barely speak, and when Nath notices that James smells of Louisa’s perfume, James yells at his son. Officer Fiske calls to let the family know that the police are ceasing their investigation and ruling Lydia’s death a suicide, which provokes an enormous argument between Marilyn and James. James leaves the house and doesn’t come back, and Nath informs Marilyn that James is probably at Louisa’s apartment. Marilyn confronts Louisa, who lies about not knowing where James is (when he is in fact there in her apartment). Knowing that Louisa is lying, Marilyn tells her that “if” she sees James, she should tell him that Marilyn will see him at home.
Three months before Lydia’s death, Nath is increasingly suspicious that Lydia and Jack’s friendship is manipulative and sexual. When the two hang out, though, they simply smoke and talk, and Jack begins teaching Lydia to drive. Lydia has now resigned herself to the fact that Nath is leaving for college, but she dreams that as soon as she gets her driver’s license she will be able to drive away and escape her family too. James gives Lydia a silver locket as an early 16th birthday present; at first Lydia is thrilled, until she sees a photo of herself inside which was taken before the 9th grade dance that James forced her to attend. On her birthday, James takes Lydia for her DMV test, which she fails. Lydia is furious, but pretends to be happy during dinner with her family. Hannah observes that Lydia is at a breaking point.
In the weeks following Lydia’s death, Marilyn confronts James about Louisa, claiming that she seems “docile” and would make a “nice little wife.” They argue and James suggests that Marilyn must regret marrying him because of how it makes her “different.” Marilyn responds that her real disappointment lies in the fact that she was forced to give up her dreams of becoming a doctor. Eventually, James leaves the house. Marilyn discovers the Betty Crocker cookbook in Lydia’s room and begins to realize that Lydia was only pretending to be interested in science in order to be close to her. Meanwhile, Nath buys whisky and drinks alone to the point of vomiting. Officer Fiske finds him and takes him home, and Fiske’s kindness is such a contrast to the treatment Nath is used to from his parents that Nath cries.
The penultimate chapter opens just days before Lydia’s death. Nath leaves for his campus visit to Harvard and, although he promises Lydia that he will call, he never does. The next night, Lydia calls Nath to ask how the visit is going and he responds to her rudely before hanging up. On the following day, Lydia wears her prettiest dress and lipstick, and after school she attempts to seduce Jack. Jack resists her advances and reveals that he is secretly in love with Nath. Although Jack explains this kindly, Lydia is furious and threatens to tell the whole school. That night, she sneaks out of her bedroom at 2am and goes to the lake. She decides that all of the problems in her life began the summer when Nath pushed her into the water, and she promises herself that she can fix everything as long as she rows out, jumps in, and swims back to shore. The last thing Lydia thinks to herself before jumping is “it will be alright.”
The final chapter returns to the period after Lydia’s death. Following his fight with Marilyn, James drives away before turning around and coming back to Middlewood. At home, he plays with Hannah, feeling overwhelmed by grief yet comforted by Hannah’s love. That night, Marilyn and James lie in bed together, feeling closer than they have for years. The next morning, Nath confronts Jack about Lydia; although Jack knows he is innocent, he lets Nath punch him. Hannah eventually pushes Nath into the lake to avoid him hurting Jack any further. In the water, Nath thinks about his permanent separation from Lydia, and all the things that will happen in the future that he will never be able to tell her. He swims toward the surface, his eyes fixed on Hannah’s face.