When it moves to present time, in a theme that will run through all the books, of Alex Cross playing his piano from his Washington DC home. The phone rings and it's his partner John Sampson, who informs him that there is another murder at Langley Terrace. Alex Cross, the Deputy Chief of Detectives, is an African-American Washington D.C. homicide investigator and forensic psychologist who also has a doctorate of Psychology from Johns Hopkins University. Cross is investigating the brutal murders of two prostitutes (mother and daughter), as well as an infant three year old boy. The women were slashed with a razor, their pubic hair completely shaved and their breasts cut off.
At Washington Day School, an exclusive school for the rich and privileged with tuition at $12,000, Gary Soneji, the mathematics teacher, interrupts the class of Ms. Vivian Kim. He tells Megan (Maggie) Rose Dunne and Michael (Shrimpie) Goldberg that the Secret Service has received a threatening call and for security reasons the children must be relocated. Goldberg is the son of the US Secretary of Treasury. Both kids normally ride together after school, so Soneji says he will take them to the drop off point for the Secret Service. Once inside his mini van he takes a small canister with chloroform. Once they are asleep, he drives off with the kids.
Alex is trying to understand this twisted and complicated criminal act of the murdered prostitutes when he is pulled off the case by his boss, Chief Pittman, to investigate the kidnapping. Cross is upset and feels that this move was racially motivated and that no one cares about dead black prostitutes.
Reluctantly, Alex and John go to Washington Day and meet Chief Pittman there. The place is full of FBI and Secret Service Agents. Alex and Chief Pittman do not get along. Their problems started over an article at the Washington Post about Alex Cross. The two argue but Pittman reveals the Mayor asked for Cross.
Jezzie Flannigan arrives on her motorcycle. She is the secret service supervisor. She had been on vacation. She arrives and yells at her 2 agents assigned to protect those 2 children, Charlie Chakely and Mike Devine. She then goes to see Mr. Goldberg who is with the Mayor, FBI Agent Roger Graham, Cross and Sampson. By now everyone knows Soneji took the children. Mayor Munroe meets with Cross later and explains to Alex why he wants him on the case and nothing Alex can say will change his mind.
That night, Soneji's van parks next to an old farmhouse, where he buries the children alive in special coffins he made for them. Soneji feels really proud of himself. Inside the house Soneji watches the television and loves to see himself. He becomes upset with what he perceives as disrespect from FBI Agent Roger Graham, as he was interviewed. Gary then goes to the bathroom and removes the brown, balding wig, then the thick mustache, and finally the contact lenses.
Later that night, FBI Special Agent Roger Graham arrives at his home when a reporter starts asking him questions. The reporter is Soneji, who takes out a knife and stabs Graham. Soneji did not like the spotlight being on Graham.
Later that night Cross, Sampson and the FBI search through Soneji's apartment, discovering Soneji's obsession with kidnappings. They also discover a note taped to a mirror with the phrase "I want to be somebody!"
Hours later Cross and Pittman get into an altercation, and then Soneji contacts the FBI, telling them he killed Roger Graham. The investigation leads the team to discover that Soneji lied about his resume and identity period. Cross meets with Maggie's parents. They also want him involved.
A few months have passed; in the meantime, the body of Michael Goldberg was discovered around Christmas time. The Dunnes’ receive a telegram from what they believe is Soneji asking for $10 million. It came from Miami. Cross, Sampson, and the FBI head down to Florida to investigate. It is in Florida that Flannigan and Cross start becoming involved.
At the same that the team is in Florida, Soneji is at a toll booth in Maryland. Soneji is disappointed in the manhunt.
At Disney World, Alex is approached by a man with a hat and jacket who said he would take him to see Maggie. Once outside, the FBI surrounded them. He threatens to have Maggie killed unless they let him go. The man takes Alex with him to the airport where they board a small airplane. The unknown man, who is also the pilot, takes off and lands the plane on a small island. At nightfall, the pilot takes off again and heads to South Carolina. There he lands, takes the money and leaves Alex there. Maggie´s whereabouts were not revealed.
On the farmhouse where Soneji kept the children, two police officers find the empty graves where Maggie and Michael were once held. Later, Gary returns to his real home, in Wilmington, Delaware where it's revealed he's married and has a daughter. We also learn that his real last name is Murphy, not Soneji, and that he was abused by his stepmother and her children.
Cross and Sampson return to Washington DC, as they are no longer wanted on the case. They are to work the murder of the dead prostitutes. By now, it's been about 6 months since the kidnapping.
Back in Wilmington, Gary begins to solidify his plans to kill his family.
Jezzie visits Alex, to let him know she was sorry he has taken the blame for the ransom gone bad.
In Washington DC, Soneji, dressed as a public utility employee, murders Vivian Kim, the teacher from Washington Day, in hopes of sending a message.
Cross & Sampson are sent to the scene, Ms. Kim has had her breasts cut off and pubic hair shaved, just like the other murders. They also find Maggie's shoe on the scene. Cross now knows Soneji is also the murderer he is looking for.
Cross & Sampson are walking the neighborhood where the hookers were murdered. They come across Ms. Scott, an elderly lady who recalls a man driving around the neighborhood several times. Ms. Scott also remembers that same man going door to door selling heating systems. Ms. Scott recalled the company was Atlantic Heating from Wilmington. Cross & Sampson are going to Wilmington.
In Wilmington, the Murphy's are having a birthday party for their daughter. Outside, the FBI with Cross & Sampson are on a stakeout. They decide to move in and rush the house. When they go in, Soneji is nowhere to be found. He managed to escape when he went to get pizza at the door from a delivery boy.
A day later Gary walks into a McDonald's and holds the people inside hostage. When the FBI hears that the man holding the McDonald's is Soneji, they rush to the scene. A trooper takes a shot at Soneji, but Alex saves Soneji, as Cross believes Soneji knows where Maggie is. Soneji promises Alex he will regret saving his life.
The trial lasts about 11 months (January when Soneji was captured until November when his verdict is read). Alex Cross is brought back to the case when Soneji asks for him. During this time Cross hypnotizes Soneji several times, speaking with both Murphy and Soneji, getting inside Soneji's/Murphy's head and gets Soneji/Murphy to tell him of all his terrible secrets. Murphy was a tender man, Soneji a sadistic, evil monster. After Soneji is convicted and put into prison, Cross and Jezzie fall in love. Despite the defenses best effort at an insanity plea, Soneji was found guilty.
After the verdict, Jezzie meets her secret lover (another man than Cross) at a lake house.
Cross returns to work and questions a woman about Soneji. She tells Cross that someone had been following Soneji. Someone knew about the kidnapping. Cross wonders about Mike Devine and Charley Chakely.
Cross meets with Soneji, who confirms he may have been followed. Soneji didn’t make the connection until he recognized the man at his trial - it was Mike Devine.
Cross meets with the FBI, they also had their suspicions and were running an investigation. The FBI believes Mike Devine and Charley Chakely took the ransom money. They believe the pilot from Florida, who has since been found dead, was a drug runner hired by Mike Devine and Charley Chakely. The FBI has no proof Mike Devine and Charley Chakely did this but still keep them under surveillance. Then they drop a bomb on Alex. Jezzie was involved with Mike Devine for years and they are lovers. They also believe Jezzie was in it from the start. Cross begins to connect the pieces. The FBI was right.
Jezzie and Devine meet. They plan to wait it out.
Cross, Sampson and the FBI begin to plan on getting Jezzie and the guys.
Soneji escapes from prison with the help of a guard that he eventually kills.
Alex takes Jezzie Flannigan on a Caribbean getaway.
In Washington DC, Soneji, dresses as a FedEx employee and visits Mike Devine. He tortures Devine to find out that the money was still in DC. Upon retrieving the money Soneji returns and kills Devine.
Alex finally confronts Jezzie and tells her he knows what she did. Since they were both wearing bathing suits, Alex showed her he wasn’t wearing a wire and demanded to know how and why. She explains that Secretary Goldberg was threatened by a Colombian cartel and demanded protection for his family. Devine and Chakely noticed Soneji making passes at the Goldberg house. Since then they followed Soneji everywhere, including the Maryland Farm. It was Jezzie's idea for the ransom, and they removed Maggie after the Goldberg boy had died. Cross demands to know where Maggie is, while, at a distance, Sampson is holding a long distance microphone. After Jezzie´s confession, Sampson and the FBI reveal themselves.
Soneji attacks Alex in his home. He planned to kill Nanna and the kids. After a fight, Soneji manages to escape momentarily, but is trapped near the White House. He is holding hostages again, this time 2 children. Soneji was about to shoot Cross, but Cross is saved by Sampson, who manages to shoot Soneji instead. Gary was wounded, but is alive.
Epilogue -- Jezzie Flannigan is executed by lethal injection. Six weeks earlier Charlie Chakely had been executed. Soneji was still alive. Due to his mental state he would be held at a mental institution. Soneji leaves Cross a letter. At the end, Cross plays the piano and heads to St. Anthony's.