The story opens with Ainsley Greenburg driving her husband, Peter Greenburg, to a couples therapy session with Joanna St. James. Ainsley describes Peter as a monster but considers herself equally compromised. Peter has become passive since learning that Ainsley knows his secrets. They check in under the aliases Pete and Annie Green, and during the session Peter uses a code word the couple agreed on, telling Joanna he is addicted to "fencing," which stands in for his criminal behavior. After the session, Peter asks Ainsley if they are going to kill the therapist, revealing that the appointment was a reconnaissance mission, not genuine treatment.
The narrative jumps back two months. Peter has found a note Ainsley planted in his secret room, a hidden, code-locked space inside their garage where he stores evidence from his crimes. Ainsley reveals she has known about Peter's double life for years, having first caught him drugging a woman at a bar when their daughter Maisy was a baby. She kept silent because she had three children, a home, and a life she refused to destroy. Peter confesses the full scope of his crimes: He has raped and killed multiple women, describing the violence as an addiction rooted in a need for control. Ainsley discloses that she framed Stefan, a man Peter had previously killed, for Peter's crimes, planting evidence to redirect the police investigation. She tells Peter she "owns" him and demands total honesty. Peter also reveals that his affair with their friend Seth was a manipulation to keep Seth quiet after Seth caught Peter with another woman.
A phone call from Ainsley's overbearing mother establishes Ainsley's fraught family history. Her mother's controlling behavior, including sending Ainsley to a weight-loss camp at age seven, shaped Ainsley's own compulsive need to manage every aspect of her family's life.
Jim Slater, Peter's former college roommate and the owner of a major contracting firm, blackmails Peter. Jim reveals that police questioned him about the secret room he built for Peter and demands to store items there. Over the following days, Jim escalates, storing a duffel bag and later a body wrapped in a tarp. Peter recalls how Jim first introduced him to violence: As college roommates, Jim drugged and raped an unconscious woman, coerced Peter into participating, then killed her. Peter describes the experience as the origin of his compulsions.
Ainsley proposes a weekend at the family's lake house to reconnect with their children: Dylan, nearly 15; Maisy, 11; and their youngest, Riley. A call from a friend leads Ainsley to discover that Maisy quietly quit dance a year ago without telling either parent because they seemed too stressed. All three children believe their parents are heading for divorce.
At the lake house, Peter opens up about the godlike power he feels when killing, admitting he fights the urge every day. Ainsley shares her painful history under her mother's control and tells Peter about Ryan, her high school boyfriend who died of a drug overdose. She sees Peter as her second chance to save someone she loves from self-destruction. She proposes an "amendment" to their existing agreement, under which each partner had been permitted to sleep with other people: Instead, she wants to help Peter kill, arguing that participating together will bring them closer.
During the trip, Dylan's girlfriend, Julie, mentions rumors about a man preying on underage girls. The conversation prompts Maisy to reveal that Coach Chris, her longtime dance instructor, has been sexually abusing her friend Bailey and attempted to lure Maisy into a similar situation. Maisy quit dance to escape him. Ainsley tells Peter they must handle it themselves.
Back home, Peter discovers Jim has filled the secret room with boxes containing fake identification documents and vials of a powerful sedative. Jim demands one night alone with Ainsley as payment for clearing the room. Peter refuses. Ainsley, who has been secretly monitoring Peter's calls, learns of Jim's threats and acts alone. She texts Jim pretending to agree to his terms, prepares the kitchen with plastic drop cloths, and slashes his throat when he arrives. She confronts Peter about his continued secrecy, furious he tried to handle Jim without her. They bury Jim together in the woods, along with the body Jim had stored in the room, and the shared act deepens their bond.
Using sedatives from Jim's stash, they kill Coach Chris. Ainsley enters the studio alone, injects Chris with the drug, and notices photographs of Chris with a girlfriend: Joanna St. James, the same therapist from the novel's opening. The discovery complicates their plan, but they proceed.
The narrative returns to the present. After the initial couples session, both Ainsley and Peter begin seeing Joanna individually without the other's knowledge. Peter becomes infatuated, eventually kissing Joanna and telling her that Ainsley is dangerous and controlling. Ainsley finds the sessions genuinely helpful and develops a kinship with Joanna, viewing her as a woman who could be destroyed for loving the wrong man. When Joanna challenges Ainsley to examine whether she truly loves Peter or is simply unable to let go, Ainsley storms out.
Joanna eventually deduces that "fencing" is not really fencing. Peter kidnaps her and holds her in the secret room, relishing the power dynamic. He withdraws from Ainsley emotionally and physically. A detective visits to ask about Coach Chris's disappearance and mentions that Chris's girlfriend, Joanna, is also missing. Ainsley plays the cooperative parent, subtly steering the investigation away from herself and Peter. When her own sessions with Joanna stop, Ainsley suspects Peter has taken Joanna and confirms it by visiting the room.
Ainsley decides to leave Peter permanently. She sedates his wine and ties him to a chair in the secret room beside Joanna, whom she has already killed. When Peter wakes, Ainsley tells him she is done trying to fix him. She outlines her plan: She will take the children on vacation, schedule a confession email from his account, and set fires to stage his death as suicide. Peter begs her to stop, but Ainsley injects him with the sedative.
Six days later, Ainsley and the children are on a beach vacation, happier than they have been in a long time. When Maisy asks when her father will join them, Ainsley says he is delayed by work. Then Ainsley's phone buzzes with a text from Peter: a photo of the room's blueprint with a circled emergency exit and the message, "Sorry, honey. We're in this together, remember? After all, rules are rules. Guess I had just one more secret. How's that for full circle?" Peter has escaped through an exit Ainsley never knew existed, and the power dynamic between them is once again uncertain. The Amendment is the second novel in the Arrangement trilogy; the story continues in The Atonement.