Quadriplegic forensics expert Lincoln Rhyme  and a patrol cop, Amelia Donaghy , team up to solve a string of murders all connected to a serial killer by his signature: a single shard of bone is removed from each of the victims. Rhyme communicates with Amelia via phone as she examines the various crime scenes and collects evidence and reports back to him. The killer poses as a New York taxi driver, and abducts and kills those who get in his taxi. The first two victims are a married couple named Alan and Lindsay Rubin, who get a taxi home but then find themselves kidnapped by the killer. Amelia finds Alan's body buried in a Civil War-era railroad bed. She also finds a piece of shellfish, which eventually leads Amelia - now working with Rhyme - to Alan's wife, and a scrap of paper. The detectives find Mrs. Rubin, too late, at a steam junction in a below ground services area of a building in the financial district, secured using old handcuffs or shackles at the mouth of a pipe which emits steam. She has been scalded to death from the steam. The killer has also removed a bit of flesh and bone from her arm. Amelia finds another scrap of paper at the scene. The killer then abducts an NYU student. He is taken to a derelict slaughterhouse where he is tied to a pole and gutted with a knife, and left for rats to feed on. Amelia and Rhyme, using the clue left by the killer at the scene of Lindsay Rubin's death , find the victim, but again too late to save him. Again, the killer has removed a piece of the victim's bone. Amelia is able to collect the evidence, including another scrap of paper. The pressure of the tense investigation and bureaucratic challenges to both Amelia's and Rhyme's involvement with the case are having serious impacts on Rhyme's health and stability. After piecing together the message the killer was sending using the scraps of paper, Amelia and Rhyme are led to an old book of short stories, which in turn leads them to the killer's next victims, a grandfather and granddaughter tied to a pier as the tide rises. The girl is rescued, but her grandfather dies. At the scene, Amelia finds another bone, an old police badge, and an old subway map. These clues, and an earlier clue left by the killer at the scene of Mrs Rubin's death  lead Amelia to an abandoned subway station, in which Amelia sees some numbers which have been tampered with to spell out Rhyme's police badge number. Amelia then figures out that the killer is after Rhyme. The killer arrives at Rhyme's house, and after killing Rhyme's nurse, Thelma , and Captain Howard Cheney , it is revealed that he is the medical technician who cares for Rhyme's medical equipment. The technician, Richard Thompson , is an ex-forensic cop who wants revenge against Rhyme, whose testimony helped convict the killer of planting false evidence at crime scenes. Rhyme manages to crush Thompson's right hand by suddenly dropping his bed horizontal, and in struggle to free himself, Thompson pulls Rhyme with him and they both collapse to the floor. Rhyme then manages to bite Thompson in the neck, causing massive bleeding. Thompson once again manages to free himself. As Thompson raises a rather large scalpel for a killing blow, Amelia suddenly arrives at the apartment and shoots Thompson dead, saving Rhyme's life. The film ends at a Christmas celebration at Rhyme's apartment. Rhyme, having given up his plans to commit suicide, faces his sister and niece coming to visit him along with Amelia and his other colleagues on Christmas Eve.