Herbert Clutter's three closest friends arrive at the Clutter home after the bodies have been removed and the police finish their initial investigation. They clean up the home and scrub it of all of the unpleasant reminders of the crime itself.
Perry and Dick have gone to Mexico, as much to avoid arrest or suspicion as to fulfill Perry's desire to go skin diving and to search for treasure. Dick goes to Mexico reluctantly and finances the trip by writing bad checks (which he calls "hanging paper"). Dick uses phony checks to get both cash and to buy merchandise, which he can sell somewhere else.
Back in Holcomb, the murders have an epic impact on the town. Holcomb is a town where people traditionally know and trust one another, but now its residents keep lights on at all hours, lock their doors, and suspect everyone else. Bobby Rupp, Nancy's boyfriend, faces more police interrogation but is eventually ruled out as a suspect — this despite the fact that he has the only reasonable motive to harm the Clutters, that of losing Nancy to her father's disapproval.
Capote reveals details of Perry's childhood. His childhood was pleasant until his mother began drinking and abandoned her husband, taking the children with her. Later, Perry was left in children's homes where he was horrifically abused, mainly by nuns. Perry is eventually reunited with his father, and they tried to start a hunting lodge, but when the business failed, Perry and his father went separate ways after an intense physical fight during which Perry felt the need to nearly choke his father to death. Perry's sister and brother both committed suicide, while a second sister established a good life for herself with a husband and children. Perry reflects on his life of crime, which mainly consists of petty thievery and breaking and entering.
Perry reveals to Dick that he has a reoccurring dream in which he is in Africa, where he approaches a tree that smells terrible but looks beautiful. In this dream, as Perry gets closer to the tree, he sees that it has diamonds hanging from it like fruit. He begins to pick the diamonds but is attacked by a giant snake that guards the tree. The snake begins to eat Perry. What Perry doesn't tell Dick is that his dream always ends the same way: with a giant bird, a "sort of parrot" arriving to save Perry, conquering whoever might be hurting Perry and then taking him to heaven.
Back in Holcomb, the murder investigation continues. Police discover a gold wristwatch tucked into Nancy's shoe, indicating that she heard the intruders and attempted to hide her valuables before they found to her. Police also note that Kenyon's Zenith radio is missing. Robbery was quickly disregarded as a motive for the crime, as Herb Clutter was infamous for having no cash on hand. But when locals hear that Kenyon's radio is gone, the townspeople presume that robbery was a motive, after all. (Capote makes it clear that Dick and Perry have possession of both Kenyon's radio and Herb Clutter's binoculars.) Finally, footprints, with a diamond shaped shoe pattern, are discovered in the basement, where Herb and Kenyon Clutter were murdered.
Still another puzzle piece that baffles investigators is the positioning of the Clutter family's bodies. Nancy and Bonnie were covered with blankets up to their chins, "tucked in" either before or after they were killed. A box had been moved from one end of the basement to the other to give Herb Clutter a more comfortable seat, and Kenyon had been given a pillow to lie on before he was murdered on the chest he built himself. These actions, coupled with the lack of apparent motive in killing the family said to be the "least likely" to ever be murdered, increases speculation in the town, criticism of the investigator, and tension within the text.
Capote introduces Albert Dewey and his family into the narrative. Albert is the lead investigator in the Clutter case, and he becomes obsessed with the Clutters, the crime scene, and with finding the killers. Albert feels haunted by the Clutter family and believes that he will remain so until he knows what happened to them. He comes to believe that the person who killed the Clutters knew them well and had a personal motive due to the intimate nature of the crime and the lack of an apparent motive. While Albert's wife is sympathetic, she is disturbed by the crime scene photos and has a terrifying dream in which Mrs. Clutter speaks to her from the grave about being murdered.
Meanwhile, Dick and Perry continue their journey. They are hitchhiking, waiting for someone to pick them up. They intend to murder the unlucky driver and then steal the car.
The townspeople refer to the unpleasant task of cleaning up after the murders as their "Christian duty." But this is also a metaphor for the townspeople's need to cleanse their town — to remove the blight on the town and to wash away the bloodshed that infected the whole town and left its people with fear and paranoia. The people of Holcomb want life to go back to the way it was before the Clutter murders. This is echoed in the townsfolk's need to find an explanation, which manifests itself in all the varied theories and rumors that further infect the town with paranoia and tension.
While on the journey to Mexico and back, Perry struggles with his role in the Clutter murders, admitting that "There's got to be something wrong with somebody who'd do something like that." He begins to "have fits" and have flashbacks of intense images, such as a shotgun blast or the voice of someone pleading for mercy. Perry does not say that he thinks that there is something wrong with him; instead he is just trying to gain some perspective on the crime, and perhaps distance himself from it. Perry seems as curious about the Clutter murders as the people of Holcomb, and as intrigued by the fact that they had no real motive to kill the family. Out of curiosity, Perry follows the media coverage of the murders, but he is not moved by it, nor does he feel remorse. Here, Capote again uses transitions and juxtaposition of character and perspective as he describes the family's funerals. From the points of view of Bobby Rupp and Nancy's best friend, Susan Kidwell, Capote includes vivid descriptions of the family in caskets, their heads encased in cotton "sprayed with a glossy substance, twinkled like Christmas-tree snow." But when Perry reads the account in the newspaper, Capote makes it clear that Perry's sole reactions are to the large turn-out for the funerals and his musings of how much money they must have cost.
Perry's compulsive self-analyses of his part in the crime and Dick's assertion that it all went "perfectly" are the only indications that the murders had any impact on their lives. During Perry's previous incarceration, his sister sent him a lengthy letter urging him to take responsibility for his actions. But Perry's friend Willie-Jay "analyzes" the letter and convinces Perry that his sister is being unfair to him. Perry clings to every word Willie-Jay says; Willie-Jay has become very much like the bird in Perry's dream, protecting him from those who would do him harm. And so in the end, Perry loathes his sister; he tells Dick that he wishes she had been in the Clutter home at the time of the murders. This indicates the deep-seated anger that Perry has for his family; perhaps he murdered the Clutters out of displaced anger for his own family.
The one woman who has had a positive impact on Perry's life is Cookie, and Capote mentions her here to illustrate Perry's disinterest in women, as well as his issues with love and his own arrogance regarding his own intellect. Perry speaks to Cookie about love and marriage, but has no intention of marrying her. When he leaves her, Perry gives Cookie a poem "he pretended to have written." This suggests Perry's need to think people view him as intelligent, cultured, and artistic, and his complete failure to achieve these things in any real way. Just a few paragraphs later, Perry is genuinely surprised to discover that perhaps Dick had only been humoring him about their trip to Mexico. Perry's innocence and naiveté are almost child-like, and this makes his later disclosures even more incredible.