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The story about the mysterious death of Lydia Lee moves back and forth in time. The story opens by announcing that sixteen-year-old Lydia—her parents’ favorite child—is dead, though her family doesn’t know it yet. The Lees live in Middlewood, Ohio. Marilyn, Lydia’s white mother, aspires to be a doctor. Her Chinese American father, James, is an American history professor. Her studious older brother Nathan is obsessed with space and headed to Harvard. And her sister Hannah, in fifth grade, is quietly observant and often overlooked. When Marilyn finds that Lydia missing, she is sure Lydia’s been kidnapped. Nathan thinks the neighbor Jack, a carefree loner who sleeps with a lot of girls, knows something about Lydia’s disappearance. The next day someone sees a rowboat in the middle of the town lake. The police drag the lake and find Lydia’s body.
The story shifts to the 1950s and provides background about Marilyn’s and James’s wishes and concerns, including how they met, married, and ended up in Middlewood. The story returns to the present with Lydia’s funeral and the Lees looking for answers. An autopsy report determines Lydia’s cause of death is drowning with no signs of foul play. James finds solace in an affair with his teaching assistant, Louisa. The story then shifts back to when Lydia was little and Marilyn hoped to resume her studies. Closing up her mother’s house after she died, Marilyn feels even more determined not to end up like her prim 1950s housewife mother. Marilyn decides to leave her family, without explanation, to finish her studies in Toledo. That summer, a young Nathan has a humiliating experience at the pool that he blames on Jack. The event reminds James of being teased as a kid, but instead of comforting Nathan, he’s hard on him, hoping Nathan will learn how to fit in.
After Lydia’s death, the Lees grieve separately. Officer Fiske indicates that Lydia may have committed suicide because she had no friends and wasn’t doing well in school. Nathan continues to believe that Jack is connected to Lydia’s death. The story then moves back to the summer Marilyn disappeared. Lost without his wife, James barely looks after Nathan and Lydia. Nathan watches a space launch on TV that ignites his passion for space. Meanwhile, Lydia promises herself she will do whatever her mother wants if only her mother will return. In Toledo, Marilyn’s aspirations are once again disrupted by pregnancy. James comes to take her home, where she decides to pour all her frustrated ambition into Lydia. Resenting the attention Lydia gets, Nathan pushes Lydia, who can’t swim, into the lake. When he rescues her, Lydia becomes especially dependent on Nathan.
Ten years later, Lydia struggles under her parents’ expectations—her mother’s desire for her to become a doctor and her father’s emphasis on having friends and fitting in. Lydia knows she is succeeding at neither. She worries about Nathan leaving her to go to college. In her physics class, which Lydia is failing, she begins a friendship with Jack. The two drive around smoking cigarettes and talking.
The story shifts to after Lydia’s death. The police close the investigation, ruling Lydia’s death a suicide. Misunderstandings pull the family apart and create further rifts between Marilyn and James. James continues to find comfort with Louisa. Meanwhile, Nathan holds on to his suspicion of Jack. But Hannah is certain that Jack didn’t do anything bad because she realized a while ago that Jack is in love with Nathan. When James doesn’t come home, Marilyn goes in search of him at school and at Louisa’s.
The story then returns to before Lydia’s death, when Lydia was spending time with Jack and Nathan was monitoring their activities from a distance. Nathan catches Lydia ripping up one of his letters from Harvard. When James gives Lydia a heart locket as an early birthday present, she feels happy at first but then sees the pictures inside—pictures of herself dressed up for a school dance that pressure her to be social and fit in—and she feels dejected and angry. On her sixteenth birthday, James and Louisa take Lydia to get her driver’s permit. In the car, Lydia realizes James is having an affair with Louisa. When she fails her permit test, Lydia blames it on the fact that she was upset, but the truth is that she just didn’t study. At home, Lydia hides the locket from James under her bed but pretends to be happy during her birthday celebration.
The story returns to after Lydia’s death. James comes home and confesses to his affair. Misunderstanding and hurt, Marilyn tells James to leave. Marilyn then angrily rips apart Lydia’s room and finds her old cookbook, which makes Marilyn realize that Lydia loved her, not science. This moment breaks down Marilyn’s walls, and Hannah is finally allowed to comfort her mother and receive the affection she’s craved. Meanwhile, Nathan takes off in the car and gets drunk. On his way to Toledo, James realizes how much he has misunderstood about Marilyn. He turns the car around to go home.
The story shifts back to right before Lydia’s death. Nathan goes to visit Harvard, and Lydia understands that he’s becoming a new person who will leave the family behind. To change herself, Lydia decides to lose her virginity to Jack. But Jack gently turns her down and admits to being in love with Nathan. Feeling foolish, Lydia threatens to tell Jack’s secret. Jack then stings Lydia by telling her that she doesn’t know what she wants.
At home, Lydia tries to figure out when everything went wrong. In the middle of the night, she decides the answer is when Nathan pulled her out of the water. Wanting to start over, this time doing what she wants and not being afraid, Lydia leaves the house and goes to the lake. There, she rows out to the middle and tries to swim back to shore, even though she doesn’t know how to swim.
The story concludes after Lydia’s death. James returns home, snuggles Hannah, and reconciles with Marilyn. Nathan sleeps after Officer Fiske delivers him home safely. The next morning at the lake, Nathan, trailed by Hannah, releases his anger and guilt about Lydia on Jack, who lets Nathan punch him. Trying to stop Nathan, Hannah pushes him into the water. Nathan wants to let himself drown but can’t. The story ends with positive references to the future and with Jack pulling Nathan from the water while Nathan keeps his eyes on Hannah’s face.