Suzanna, the novel's narrator, grows up visiting her mother, Helen, at Hillcrest, a women's federal prison perched on a steep hill. Each Saturday, Suzanna's grandfather Joe drives her to the prison, where they climb the hill together. Joe sits at his own table during visits while Suzanna waits in the Children's Center, a room run by three nuns: one deaf, one mute, and one nearly blind. Helen arrives through the inmate door and presses Suzanna's head to her chest. Between Joe and Helen, a vow of silence exists. Suzanna's grandmother Sylvie refuses to go anywhere near the prison.
The year Suzanna turns eight, the prison expands: A hospital, gun tower, cemetery, and nursery go up, and fences grow taller. New legal rulings cause women Suzanna expected to stay forever to descend the hill and leave. During one visit, cats attack Joe after he moves a dead deer off the road. At the base of the hill, Suzanna tells her bloodied grandfather to stay behind and climbs alone for the first time. At the summit, she vows to return every week, to become a great stayer rather than a leaver.
The winter Suzanna turns nine, Joe dies. Sylvie refuses to take Suzanna to the prison, calling her refusal "justice" and "freedom," blaming Helen for Joe's death. Suzanna moves into Sylvie's bed, and they watch the news in a room without clocks. Helen's phone calls grow shorter as Sylvie coaches Suzanna to deflect. The hill begins to feel unreal, and Helen becomes more occasional and farther away.
One morning, Sylvie takes Suzanna to the bank Helen robbed. She reveals that Helen sat in the car while her accomplices went inside and a security guard was killed, then describes the alternate life they could have had: Joe alive, Sylvie still working, Suzanna visiting her grandparents only occasionally. She sends Suzanna to see the guard's memorial plaque, but Suzanna will not go past the vestibule. Sylvie drives away, leaving Suzanna stranded for hours. When she returns at closing time, she will not unlock the car, saying through the glass, "I can't." On the drive home, Sylvie voices her longing for her old life. That night Suzanna resolves to sleep in her own room. In the morning, Sylvie looks frightened and impressed: "It's not too late for you yet, Suzanna."
Helen arranges for Sister Claudine, a nun devoted to reuniting families, to drive Suzanna to the prison. Sister Claudine campaigns to bring Sylvie up the hill, but Suzanna cannot comply. On Suzanna's first visit back, Helen keeps one part of her body touching Suzanna at all times. In the Reading Roost, a cubby with curtains painted as the mouth of Jonah's whale, Helen begins telling stories from her past: Sundays at Coney Island with Joe. Suzanna realizes Joe had taken her to the same places without mentioning Helen. Sister Claudine tells Suzanna about a woman kept in solitary confinement for ten months, denied all clocks, who could only ask, "What time is this?" Suzanna resolves never to let her mother go unvisited.
After a year, Suzanna gives up on bringing Sylvie and pledges herself to life as it is. Sylvie decides Suzanna will skip seventh grade. Suzanna, now the shortest and youngest in her class, moves through the schoolyard with speed and purpose so no one notices she has nowhere to go. At twelve, she begins taking the train to the prison alone. A volunteer at the Children's Center declares her too old to stay, and she is exiled to the main visiting room. On the first day of high school, Sylvie stands on the terrace watching Suzanna walk to the subway until she descends underground and disappears.
Companion puppies arrive at Hillcrest. Helen initially refuses the program because it requires a month without visits. After a pipe breaks and floods the visiting room, an officer unlocks the courtyard and everyone streams outside, the first time Suzanna steps outdoors with her mother. Visiting shuts down for repairs; Helen gets her puppy, and Suzanna gets her first free Saturdays. Helen's training regimen spills into her interactions with Suzanna. She dislocates her shoulder playing with one of the dogs and loses her place in the program. Suzanna begins leaving visits early, following her favorite officer, Harris, to the train, feeling she is protecting him.
During Suzanna's sophomore year, Sylvie develops persistent chest pain. A letter arrives from Helen addressed to Sylvie for the first time, and Suzanna knows her grandmother must be dying. Sylvie refuses to read it. She develops a cataract that leaks milky fluid down her cheek, and a murder trial on Court TV becomes her only measure of time. A visiting nurse tears open Helen's letter and reads aloud; Sylvie thrashes and bellows. Suzanna refolds the pages without reading them. Nightly, Sylvie asks for all her pills; Suzanna gives her two. Sylvie demands Suzanna burn everything after she dies and makes her promise not to have children.
In her final days, Sylvie shares stories from Moscow. A cat in their apartment fell out a window and died. Sylvie told toddler Helen the cat had gone searching for her, but she overheard Helen telling a neighbor boy the truth while asking him not to tell her mother. Realizing her daughter understood what was actually happening, Sylvie decided to leave the Soviet Union. Helen calls constantly. One night Sylvie accepts the charges. Suzanna hears Helen say "Mama? Mama?" through the receiver. Sylvie does not speak and hangs up. Together they carry out the burning on the terrace: nine garbage bags of papers, photographs, and letters. Sylvie throws her wig into the embers, and it catches fire and sweeps over the railing. On her last night, Sylvie tells Suzanna about her own mother seeing them off at the port of New York, crying, touching baby Helen's face. Six days later, Sylvie dies.
A few days after Sylvie's death, Suzanna spends two nights in a trailer on the prison grounds, her first time inside the prison overnight. The officer who announces counts every three hours disappears, and the silence unsettles them. In the dark, Helen reveals that during her first months in solitary confinement, Sylvie sent three letters with survival instructions that saved her life. In the morning, an officer retrieves Helen. She hoists her transparent backpack and walks toward the other women. Suzanna is left behind in the trailer, forgotten.
In her senior year, Suzanna is placed at the Museum of Natural History through an internship for students who did not apply to college. Jean, Sylvie's closest friend, offers Suzanna her apartment and Batsheva's old bed but pushes her toward independence. Jean once saw her late daughter Batsheva in a diner but did not approach her. Helen also pressures Suzanna to leave: "Take a break, Suzanna. Go adventure. I'll be here."
On a Saturday train ride to the prison, the train fails to stop at scheduled stations, rushing past platform after platform. Suzanna considers keeping going. The train passes Hillcrest easily and fast. When it finally stops several stations past the prison, Suzanna begins the long walk back. The gun tower emerges in the distance and she feels homecoming. At Processing, the prison's security checkpoint, the guard types Helen's number into the system. "No, she's not here," he says. "No, that one is gone."
The final chapter shifts to Helen's letters from what Suzanna calls "the traveling years." Helen has been transferred through five prisons in five states before being flown to a men's facility in Arizona. Hillcrest has shut down entirely. Helen writes of the desert and twelve women she hears but never sees. On the plane, a parrot walked down the aisle on a leash, and Helen thought of her mother. She reveals a final image: during her transfer out of Hillcrest in the early morning dark, she looked through the van's barred windows and saw a figure climbing up the hill through the steam. She watched the figure ascend toward the tower's light as the van descended. "I'm out," she wanted to shout. But the hill curved out of sight.