Part 2 of the novel begins in Amy's voice, speaking to the reader on the day of her disappearance. She reveals the shocking secret at the heart of the novel: she has faked her own disappearance, making it look convincing through actions such as cutting herself and bleeding on the kitchen floor, staging the living room to look as though a struggle has taken place, leaving behind the box with the treasure hunt clue, sneaking out of the house without being seen, and driving away from Carthage. Amy reveals not only this secret, but a different perspective on her personality and history. She was born after her parents suffered many miscarriages and stillbirths, and therefore they were both very proud and demanding of her. When she met Nick, she performed a version of herself that she believed he, like all men, would like: the Cool Girl. She genuinely loved Nick at first, and they enjoyed a period of happiness. However, as Amy began to reveal her true self, Nick withdrew, and the marriage started to fall apart.
A major blow was dealt to their marriage when Amy saw Nick and Andie kissing. Enraged, she decided to frame him for murder and starts laying her plans. She takes careful steps involving buying a car and hiding it to use as her getaway car. She also writes the diary, dating it to look as though she has been keeping it for a long time, and crafting a narrative in which she is sweet and likeable while Nick is violent and dangerous. Once she leaves Carthage on the day of her disappearance, she cuts and dyes her hair and puts on a pair of glasses to alter her appearance. She drives to a rented cabin in the Ozarks, gloating about how successful her plan will be, and looking forward to using the media coverage to follow the story and watch Nick suffer. She has saved about $10,000 to live on while she hides out, and once she has seen Nick arrested and charged, she plans to kill herself so that her body will be found and confirm his guilt. She is sure that the combination of Noelle revealing her pregnancy, the police discovering the diary, and Andie eventually revealing the affair will make Nick appear guilty.
Amy is pleased when Noelle reveals her pregnancy at the vigil, since this was a particularly difficult part of the plan. In order to fake her pregnancy, she tampered with her toilet so that it wouldn't flush, and after Noelle (who actually is pregnant) came to visit and urinated into the toilet, Amy stole some of the urine. She then made a doctor's appointment and passed the urine off as her own, claiming that she could not have a blood test due to a phobia of blood and needles. While staying at the cabin, Amy tries to be as discreet as possible, but can't help stirring up interest from the residents of the other cabins. In particular, a young woman named Greta strikes up a friendship with Amy, and the two watch the episode of Ellen Abbott together. Although Amy is confident in her disguise, she cannot help but fret that Greta is on to her true identity.
Greta makes friends with a man named Jeff, also staying in the cabins. As Amy spends time with the two of them, her plans change, and she decides she no longer wants to kill herself. The problem is that her funds are already rapidly dwindling. Amy is so desperate for money that she goes with Jeff to earn some money by catching catfish.
Meanwhile Nick is horrified to discover that the woodshed is filled with various expensive items purchased using the credit cards that Amy opened. He has also realized what all the sites of the treasure hunt have in common: they were all places that he and Andie had sex. Realizing that Amy must have known he was cheating on her, he believes that she is deliberately framing him for her murder. He shows Margo the shed, and explains his theory to her. They find the final gift-wrapped package and open it together, uncovering two antique puppets. They figure out the puppets are Punch and Judy dolls, characters from an old puppet show, in which the husband kills both the wife and child. The narrative Amy has created, which makes Nick look guilty, suggests that he was furious when she found out she was pregnant and killed her as a result.
Nick calls Tanner to share his theory that he is being framed. Late that night, awaiting Tanner's arrival, Andie shows up at Margo's house. Nick, increasingly worried about their affair being revealed, ends the relationship with her and she reacts badly, leaving the house angry and upset. The next morning, Detective Boney comes to visit him and tells him that Amy's purse has been found, discarded in such a way to look like whoever abducted her tried to hide it. The detectives, however, suspect that the disposal of the purse was staged. A short time later, Tanner arrives, and Nick lays out his theory, explaining that he believes Amy is both fabricating his guilt and toying with him at the same time. Tanner, Nick, and Margo go to Nick's father's house to search for any other incriminating evidence, but cannot find anything. Nick suggests telling the police that he is being framed, but Tanner points out that in order to do so, they would have to reveal the affair, and that doing so could hurt Nick's case. Nick also finally reveals where he actually was the morning that Amy vanished: he sometimes sneaks out to read old copies of the magazine he used to work for.
Nick returns to the house, which by this time is besieged by journalists. Amy's parents are upset that Nick has hired Tanner Bolt, since the Elliotts associate Bolt with representing guilty parties. Marybeth lashes out against Nick, accusing him of having hurt Amy. Frustrated, Nick calls Tommy O'Hara, Amy's ex-boyfriend, and the two men speak on the phone. Tommy explains his history with Amy: the two dated, but he quickly became disinterested. Tommy was reluctant to completely end the relationship, so he led Amy on while also seeing another woman. When Amy found out, she was furious, and managed to frame Tommy for rape after having consensual sex with him. Tommy was terrified, and after Amy dropped the charges, she sent him a threatening note. After the conversation with Tommy, Nick phones Hilary Handy. Hilary tells a story of an intense relationship with Amy that soured after Amy became jealous of Hilary. Amy then injured herself and claimed that Hilary pushed her down the stairs, resulting in the impression that Hilary is an obsessed stalker. Nick presents these conversations to Tanner as evidence that Amy is capable of elaborate lies and deceptions, but Tanner finds the evidence unimpressive.
Left alone, Nick reminisces about his desire to have children, and how Amy always vaguely delayed the possibility of having a baby. After the layoffs, Amy had stopped using birth control, and when she had not gotten pregnant within a few months, the couple went to see a fertility doctor. Nick collected semen to use for artificial insemination, but then Amy abruptly announced that she did not want a child after all. After a year, the clinic disposed of the frozen semen. Feeling increasingly depressed, Nick leaves the house and goes to the bar. Nick is approached by a young woman named Rebecca, who strikes up a conversation and buys him drinks. Rebecca writes for a true crime blog and wants to get a statement from Nick. Nick praises Amy, describing how much he loves his wife while hating her inside.
In the novel's second part, both Nick and the reader reach a shocking realization: Amy has deliberately orchestrated her own disappearance and is framing Nick as punishment. While much of the novel's first section suggests that Nick was the one lying and being deceptive, it now becomes clear that Amy is an evil genius who has carefully constructed an elaborate plan. This discovery is particularly shocking because women, especially physically beautiful ones, are often presented as the victims in crime narratives, and this discovery reverses that trope.
The novel's second part reveals that Amy, in reality, is nothing like the woman depicted in the diary. Nick's perception of her was somewhat accurate, but she is more warped and cunning than he ever could have imagined. Amy's childhood left her with an obsessive need to be perfect and control everything around her, and she could not handle the fact that Nick was a mediocre, average man. While Amy is capable of doing terrible things and ruining people's lives, she is also impressive. Amy is clearly extremely intelligent, detail-oriented, and strategic. It seems like a tragic waste that her abilities were not being utilized in some other way. Indeed, Amy was able to dream up and carry out her plan because she had nothing else to do. Although someone who did not have Amy's disturbed personality would not have come up with such an idea, there is a connection between boredom, a lack of opportunities for women, and the devious ways she uses her intelligence. After reading the novel, a psychologist named Dr. Ryan Niemiec wrote an article discussing Amy's actions from the perspective of the psychological theory of "strengths misuse." This term "refers to those times when individuals deliberately use their character strengths to manipulate or harm others. This is not only the dark side, but the 'darkest' side of character" (Niemiec).
Amy is acutely aware of how women are viewed by society and by men. She manipulates these stereotypes to her advantage. For example, when she first meets Nick, she pretends to be easygoing, fun-loving, and spontaneous, even though that is not her nature. This fabrication and deception sets her marriage up for tragedy because Nick doesn't know the real her, and therefore can't love her for herself. However, Amy still feels that if she wants to win Nick's heart, she has to model herself after this stereotype.
Amy also relies on female stereotypes in order to make the diary an effective tool. She knows what kind of woman the world likes: sweet, optimistic, self-sacrificing, and considerate. By creating a version of Amy who exemplifies these traits, she ensures that when the diary is read, people will feel protective of her and turn against Nick. The diary is a particularly interesting aspect of Amy's plan because it reminds the reader that written narratives cannot necessarily be trusted. Just like the diary could turn out to be a masquerade, a story can always turn out to be more complicated than it appears.
Nick's discovery of what his wife's actions is a horrifying moment for him, but it is also the first time he really sees her for her, and understands what she is capable of. In a sense, it is the discovery of Amy's plot that creates the intimate knowledge one would expect to find in a marriage. Nick begins to gather information that casts a dark light on Amy, suggesting that she has a long history of lies, manipulation, and deception. He also begins to develop his own plan. Nick knows that he needs to lure Amy back to him and that, in order to do so, he will have to pose as a loving husband. When Nick begins to lie and give a false impression of how he feels about Amy, he paradoxically becomes more like her. He is now also plotting and scheming out of hatred towards her.