Washington, D.C. homicide investigator and forensic psychologist Alex Cross investigates the brutal murders of two black prostitutes and an infant. Then, at an exclusive private school, math teacher Gary Soneji kidnaps Maggie Rose Dunne and Michael Goldberg. Cross is pulled off the murder case to investigate the kidnapping instead. Angry because he feels everyone cares more about two rich white children than three dead black people, he meets Jezzie Flannagan, the head of the children's Secret Service detail. At an old farmhouse, Soneji buries the children alive in a specially made coffin. Angered by FBI agent Roger Graham's contemptuous comments about him on TV, Soneji later impersonates a reporter and kills Graham. Meanwhile, Cross, his partner John Sampson and the FBI search Soneji's apartment, discovering his obsession with kidnappings, particularly that of the Lindbergh baby, and his desire to become a world-famous criminal.
Some time later, Michael Goldberg's corpse is discovered, and the Dunnes receive a telegram demanding $10 million. Cross, Sampson and the FBI investigate, and Cross begins an affair with Jezzie Flannagan. He is ordered to deliver the money to Walt Disney World in Orlando, wondering how Soneji knows about his involvement. A man takes him on a plane, flying to a small island and taking the money, but never delivering Maggie Rose. At the old farmhouse, police officers find the empty graves where the children were held. Soneji returns to his home in Wilmington, Delaware, where it is revealed he has a wife and a daughter.
In Washington DC, Soneji, dressed as a public utility employee, murders a teacher from the private school. Cross and Sampson are sent to the scene and, seeing the way he mutilated the body, quickly realize that Soneji is also behind the killings they investigated before and after the kidnapping. In the murdered prostitutes' neighborhood, an elderly woman recalls a man going door to door selling heating systems. They soon find out that a man named Gary Murphy works for the company, and put observation on his family home in Wilmington, but Soneji manages to escape. A day later, he walks into a McDonald's and holds several people hostage. Soneji is almost killed, but Cross saves him, as he believes Soneji knows where Maggie is. The criminal promises Cross will regret saving his life.
The trial of Gary Soneji/Murphy lasts eleven months. Cross hypnotizes him several times, learning he seems to have a split personality; Gary Murphy, his everyday persona, is a gentle family man, while Gary Soneji is a vicious sociopath. Despite the defense's best effort at an insanity plea, Soneji is imprisoned. Meanwhile, Cross learns that someone was following Soneji and knew about the kidnapping. Cross suspects Mike Devine and Charley Chakely, the Secret Service agents in charge of protecting Maggie Rose and Michael when they were kidnapped. He meets with Soneji, who confirms he may have been followed. He did not make the connection until he recognized the man at his trial: Mike Devine.
Cross meets with the FBI, who have believed for some time that Devine and Chakely took the ransom money, hiring and later murdering the pilot from Florida. Cross also learns that no other than Jezzie Flannagan masterminded the kidnapping using her lover, Devine, as a pawn. Around the same time, Soneji escapes from prison and goes to Washington, where he tortures Devine to find out where the ransom money is. After retrieving the money, he kills Devine.
Cross takes Flannagan on a Caribbean getaway, and confronts her about her actions. She explains that Devine and Chakely noticed Soneji driving by the Goldberg house, and followed him. The ransom was her idea, and they removed Maggie Rose after Michael died accidentally. Flannagan is arrested based on a recording Sampson made of the conversation, and Maggie Rose is found with a family in South America, where she had been living for the past two years.
Shortly after this, Soneji attacks Cross at his Washington home, attempting to kill his grandmother and children. Losing the fight, Soneji is hunted through the capital and eventually cornered on Pennsylvania Avenue, where he takes two children hostage. Soneji is about to shoot Cross, but Sampson shoots Soneji first, wounding him. Some time later, Charley Chakely and Jezzie Flannagan are executed for their crimes, while Soneji is locked up in a mental institution. He writes a last taunting letter to Cross and bribes a guard to leave it on Cross' windshield. Disturbed but unwilling to let the psychopath disrupt his life any further, Cross returns home to spend time with his family.