Eden Lowenstein is 13 the day she's kidnapped by a man in an old blue truck. She's always been called Alice Ringwald. At least, that's who she's been for the past six months while she's lived with her foster family. She can't remember anything before that time. Then a scraggly but kind-eyed man named Wyatt knocks on the door. He tells her in hushed tones that he's married to her birth mother, and he's come to take her home. When she won't comply, he apologetically ties up her foster mother and pleads with Eden to go with him. He promises she can return if she wants but says her mother is desperate to see her.
Confused but curious, Eden goes with Wyatt. They hide out in a cabin for several days while the FBI launches an investigation into the girl's disappearance. The lead agent, Olivia Strauss, is particularly drawn to the case in light of her own demons. She lost a daughter Eden's age and still blames herself. Olivia learns that a high-ranking politician had an affair, and Eden was the result. To keep the situation quiet, the man had Eden put up for adoption and her mother, Kathryn, institutionalized. FBI records indicate that Kathryn committed suicide, but Olivia still suspects the birth mother is responsible for the abduction. Olivia also learns that Eden was one of 35 children who grew up in a monastery as part of an experiment. Some of the children could affect the world in ways that border on the paranormal. (When the experiment couldn't be controlled, it was shut down and the children's memories were wiped clean.)
Eden and Wyatt finally arrive at "home" in a Louisiana swamp. The house is part of a compound consisting of 11 homes. The landowner, Zeke Gunner, runs a moonshine business and has set himself up as a "god" over the families on his property. From the start, he reminds Kathryn that he's the one who has helped her get her daughter back. She owes him everything. Kathryn is overjoyed to see Eden. But from the start, Eden knows something is wrong. She meets her younger brother, Bobby, and loves him instantly. But she can tell his mind doesn't function as a normal child his age. Kathryn rambles on about God bringing Eden back to them and about her purity. She repeatedly calls Eden the spotless lamb.
The first night at home, Eden tries to run away, but standing out in the night, surrounded on all sides by swamp, lake or Zeke's dangerous dogs, she knows she's trapped. She also realizes she has to stay to protect Bobby.
Kathryn starts by scrubbing and cleaning Eden thoroughly. Eden doesn't know whether to be disturbed or to consider this a gesture of love. Kathryn then begins a weekly ritual in which she baptizes Eden and lightly, symbolically, beats Bobby while cursing him. Bobby, she explains, was a punishment for her (Kathryn's) sins. She briefly tells Eden about her own childhood. Her religious, wealthy father gambled away all their money and killed himself. Her mother started drinking, so child protective services put Kathryn in an orphanage. Later, Kathryn's own child, Eden, was hidden from her. The sins of her father were a burden they were all still bearing, she said. But Eden's purity would keep them all pure.
Kathryn demands many things of Eden. She carefully chooses the girl's food and requires Eden to keep her arms, legs and feet entirely covered. Sometimes she locks Eden in the closet or forbids her to sit on furniture or say certain words for several days in an effort to keep the girl from becoming inattentive. Kathryn quotes Scripture often, frequently out of context. She calls Zeke an apostle, but it's clear he is essentially her god.
Olivia continues to follow leads on Eden's case but comes up empty. A man calling himself Stephen visits her office to talk about the case. Something in his eyes speaks to her soul. He tells her Alice (Eden) isn't ready to be found yet. He also tells Olivia she's got to forgive herself for her daughter's death and find freedom. He leaves behind a calling card with one word: Outlaw.
Five years pass. Eden has become accustomed to the strange life with Kathryn. She even starts to believe Kathryn's rituals purify her. Zeke calls Kathryn to his house and informs her of a trust Eden's birth father set up before his death. The fund is now worth more than $1 million, and he insists it must be turned over to him since he gave Eden back to Kathryn. Kathryn is pleased that the money will bless them all, as Zeke says. They cautiously take Eden off of their property for the first time to sign papers in town. Eden doesn't hesitate to turn the money over to her mother because she has no use for it anyway.
Eden begins having vivid dreams in which she meets Outlaw. He urges her to overcome her fears by going out on the water in his boat. In cryptic but loving ways, he tries to plant the idea that Eden must be strong enough to find her way out of her circumstances to freedom.
Mother warns Eden about purity of mind now that she's getting older, and Eden feels guilty for not telling Mother her feelings for Zeke's son, Paul. She sneaks around to see Paul twice, and he kisses her on the cheek. When Zeke finds out, he brutally beats his son and threatens Eden. Eden's eyes are open to the injustice all around her. She begins to see how Zeke is using her for her inheritance money. She becomes increasingly angry with him, her mother and all of her circumstances. When Kathryn learns about Paul's kiss, she knows she must do something drastic to avoid Zeke's wrath. She chops off Eden's long, beautiful hair and tells Eden the list of confinements she will face until she repents.
Eden attempts to escape with Bobby that night. Wyatt provides keys to the truck. Zeke's men thwart the attempt. Zeke sends Wyatt away for his part in the escape. Then he tells Kathryn she must do what a good shepherd would with a wayward sheep: She must break Eden's leg. Kathryn injects Eden with the substance Zeke gives her to paralyze the girl. But Kathryn can't bring herself to break her daughter's leg. She finally decides to sprain it a little and set it so it looks like it was broken. She hopes this will fool Zeke. When Eden unsuccessfully tries to escape a few days later, Zeke learns Kathryn failed him. He comes to their home and breaks Eden's leg himself.
Eden dreams of Outlaw again, and he's urging her to walk on the water. He explains that she must not let her circumstances, the rushing waves all around her, be what define her. He convinces her that, if she wants to be free, she must forgive all of the offenses and people who have hurt her. She realizes he's right and emerges from the dream a different person.
When she wakes up, she can understand all the ways life damaged Kathryn and the abuses her mother suffered. She offers genuine forgiveness to Kathryn, who is overwhelmed. They both see that Eden's leg has miraculously healed. Kathryn finally realizes everything must change drastically now, including her. She drives to Zeke's house, hits him over the head with a skillet and ties him up before calling 911 to report the kidnapping of five years earlier.
As the book ends, Olivia sits with Eden, Kathryn and Wyatt in their living room. Zeke has been arrested on a number of counts. While Eden doesn't want to press charges against her mother (or her father for earlier offences), there is still some question about the consequences they will face. Eden goes outside to find Bobby skipping stones with Outlaw. She feels as though she has found peace at last and is finally home.