Urged on by Marshall, he kills a couple and, as part of his pathology, leaves each of the victims' bloody thumbprints on a lampshade. Brooks follows his meticulous modus operandi, including fastidious preparation and cleaning up the crime scene before departing. Marshall then notices that the couple's curtains were open.

Brooks' daughter Jane (Danielle Panabaker) appears, having dropped out of college. She goes on to visit Brooks at work and mentions that she would like to get a job with his company. The same day, “Mr. Smith” (Cook) turns up at Brooks' work and attempts to blackmail him with photographs from the most recent murder. He demands that Brooks take him along on a murder; reluctantly, Brooks agrees.

Mrs. Brooks (Marg Helgenberger) reveals that Jane dropped out of college because she is pregnant. The Brookses are then visited by detectives from Palo Alto who want to interview Jane about a hatchet murder committed in her former dorm building. Marshall and Brooks realize Jane committed the murder and consider letting her go to jail to "save her" from becoming like them. Eventually, however, Brooks decides to use an alternate identity, fly to Palo Alto, and commit a similar murder to make it look like a serial killer is loose, thereby exonerating Jane.

Brooks decides that he no longer wants to kill, but knows that he cannot stop himself. Not wanting to be caught and shame his family, Brooks concocts a plan where he will write a note to his family claiming to be terminally ill, and leave, never to return.

Brooks researches the background of the police officer chasing the "Thumbprint Killer," Detective Tracy Atwood (Moore), and discovers she is in the middle of a messy divorce from Jesse Vialo (Jason Lewis). Brooks decides that Vialo will be Smith's first "victim." At the scene of the Vialo murder, Smith urinates in a fit of panic, leaving his DNA at the scene for the police to discover later. While driving away from the scene, Smith pulls a gun on Brooks, which Brooks and Marshall had predicted would happen. Brooks explains his plan to Smith, who agrees to kill Brooks. Brooks takes Smith to a cemetery he owns, and explains that they will find an open grave. Smith will shoot Brooks and then cover him with just enough dirt to mask the body. The next day, a casket will be lowered into the grave and covered, and Brooks' body will never be discovered.

Smith attempts to shoot Brooks, but Brooks reveals that, at some point prior, he had broken into Smith's apartment and bent the firing pin on Smith's pistol, rendering it inoperable on the off-chance that Brooks would change his mind. Brooks' brush with death makes him realize he wants to see his grandchild, and he turns on his would-be murderer. As Smith desperately tries to make his pistol work, Brooks beats him to death with a shovel. As Smith lies dying, Brooks reveals that he used many different MOs before becoming the "Thumbprint Killer." With Smith's urine providing the only DNA evidence of the Thumbprint Killer at the murder scene, Brooks remains undetected.

Mr. Smith is named as the Thumbprint Killer and Brooks returns to his normal life. Knowing he is in the clear, Brooks calls Detective Atwood, whom he has come to admire, to ask her why she is a police officer. She replies that her father had wanted a boy, and she wanted to succeed in spite of him. Atwood is unable to trace the call before Brooks hangs up, but she realizes the Thumbprint Killer is still alive. That night Brooks has a nightmare in which Jane kills him, suggesting that he fears Jane will become like him.