Plot
In 1998 New York City, forensics expert Lincoln Rhyme is bed-bound after an accident that left him quadriplegic. Amelia Donaghy, a newly recruited patrol officer, discovers a mutilated corpse buried at a Civil War-era railroad bed. Rhyme directs her through a free video/audio feed sent from Donaghy to him in his bedroom. Due to clue-like objects found at the crime scene, Rhyme concludes that the scene was staged. Impressed by Donaghy's forensic instincts, he teams up with the young officer.
The killer poses as a taxi driver and, before Rhyme and Donaghy meet, abducts married couple Alan and Lindsay Rubin. Donaghy discovers Alan's body at the railroad station. Lindsay is revealed to be alive and tied up at a steam junction. Using the clues found at the railroad bed, including a torn piece of scrap paper, Rhyme successfully tracks the whereabouts of Lindsay. The detectives and Donaghy arrive but are unable to prevent Lindsay from being scalded to death by an open steam pipe. Donaghy finds a piece of bone by her body and another scrap of paper. Rhyme instructs Donaghy to sever Lindsay's hands in order to obtain evidence, but she refuses and storms off.
The killer abducts an NYU student, who is taken to a derelict slaughterhouse, tied to a pole, and left with an open wound that attracts nearby rats. Donaghy and Rhyme, again using the clues left by the killer at the scene of the previous murder, find the victim's body mutilated by rats. Donaghy finds another scrap of paper and a piece of bone. The pressure of the tense investigation and bureaucratic challenges to Donaghy and Rhyme's involvement in the case begin to have serious effects on Rhyme's health and stability. Thelma, Rhyme's caregiver and nurse, reveals to Donaghy his plans to end his life out of fear of seizures that could leave him in a vegetative state.
After piecing together the message the killer was sending using the paper scraps, Donaghy and Rhyme are led to an old crime novel called The Bone Collector, which details crimes the killer is replicating. The fictional outline leads them to the location of the next victims, a grandfather and granddaughter who have been tied to a pier during a rise in tide. The paramedics successfully resuscitate the young girl, but the grandfather dies. At the scene, Donaghy finds another piece of bone, part of an old police badge, and a subway map. These clues together with the asbestos left by the killer at the scene of Lindsay's death lead Donaghy to an abandoned subway station, where numbers on the side of a carriage have been tampered with to spell out Rhyme's police badge number.
Police captain Howard Cheney arrives at Rhyme's house with the intention of halting the investigation but is murdered by the killer alongside Thelma. The killer is revealed to be Richard Thompson, the medical technician in charge of Rhyme's medical equipment. Richard's real name is Marcus Andrews, a former forensics expert convicted because an article written by Rhyme exposed Andrews for planting evidence that resulted in the wrongful imprisonment of six innocent people, one of whom hanged himself. Maintaining his delusion that he was right to imprison those people, Andrews blames Rhyme for his imprisonment and the abuse he endured during his incarceration and has schemed to humiliate Rhyme by testing his abilities in a game of wits before killing him. Rhyme manages to crush Andrews' hand in his medical bed and further harms him severely by biting his neck. Unable to move, Rhyme is about to be stabbed to death by Marcus until Donaghy arrives and shoots him dead. The following Christmas, Rhyme, having abandoned his plans to commit suicide, meets his sister and niece coming to visit him, along with Donaghy and other colleagues.
