The rising action starts early as Nancy's children vanish and continues throughout the middle of the book; each new revelation, such as Nancy's mental issues as a student and how they might affect her life, adds to the suspense of the book.

The major conflict is Man versus Society; Nancy knows herself to be innocent, but has no proof and is the victim of prior accusation. Her quiet, isolated nature makes her more likely to be mentally ill in the eyes of Society.

She'd come to Cape Cod because she'd always heard that... Cape people were reticent and reserved and wanted nothing to do with strangers, and that was good. She needed a place to hide, to find herself, to sort it all out, to try to think through what had happened...
(Clark, Where Are The Children?, Google Books)

Throughout the novel, Nancy fights against the majority opinion, that she has major mental problems that cause her to be violent against her children, and it is only after the final revelation that she is thematically victorious over Society.

The climax of the novel occurs near the end, when it is discovered that Courtney Parrish, a recluse living in an old house, is actually Nancy's first husband, who had faked his own death. He had been molesting their daughter, and killed both children to cover up the crime; now, he seeks to make Nancy the undeniable guilty party and escape judgement himself. This revelation allows Nancy to finally reach closure for the deaths of her first two children.