Dick and Perry are incarcerated and await trial. Dick is put into the county jail, but in order to keep the two separated, Perry is put into a cell usually reserved for women at the home of the undersheriff, Wendle Meier, and his wife. Perry befriends the couple, who treat him well, and he acquires the trust and affection of a wild squirrel that lives just outside the window. When asked to sign his statement, Perry asks that it be changed to reflect what he now asserts as the truth: that he killed the entire family and that Dick did not kill Mrs. Clutter or Nancy. Perry does this as a means to comfort Dick's mother. He also keeps a journal, remarking on his upcoming trial and his current life with the Meier's.
Dick lives among the general population in county jail. He becomes popular among the inmates and begins to plot an escape. He fashions a shiv, but it is discovered before he can enact his plan. Perry also begins to think about escaping and he writes a note to two young boys who have been watching his cell, asking for a hacksaw. After he writes the note, Perry never sees the boys again and he begins to wonder if they ever existed. Perry also considers suicide by using the light bulb in his cell to cut his wrists. In a dream in which he succeeds in killing himself, he is visited again by the yellow bird.
The trial arrives, and Perry and Dick's sanity is called into question. The first doctors who examine Perry conclude that he is now, and was at the time of the murders, sane by the legal definition.
Further details regarding the behavior of the two men following the murder are recounted. Perry says that after the killings the two men couldn't stop laughing, that they felt "high" and joked around as they buried evidence and cleaned themselves. This new physical evidence was found by investigators and brought to the trial, along with the radio, binoculars, and photographs of the shoe prints matching those of Dick and Perry. With this, even without the confession, the case is solid. Each man is appointed a lawyer; both lawyers confess that the case is not the most attractive to a defense attorney, but they do their best to represent Dick and Perry.
Perry begins to correspond with Don Cullivan, a man with whom he served in the army. Don eventually comes to visit Perry in jail, and the two of them share a meal. Perry tells Don that, in truth, he is not sorry and feels no regret for his crime. Don, a Christian, tells Perry that he is concerned for Perry's soul. Don admits that he enjoys Perry's company and friendship, and personally concludes that it is only because of God's grace that he, himself, did not end up a criminal in the same way that Perry has.
The property and belongings of the Clutter family are auctioned off. There is a large turnout, and everything is sold. The final tragedy is the sale of Babe, Nancy's horse, who was not a useful farm animal, but a pet. Sue Kidwell is overcome at the sight of Babe being led away by a farmer intending on using the horse to plow.
Floyd Wells testifies as the "mysterious" witness. He is given the reward, but at the time of the book's writing, he is again incarcerated for armed robbery. The prosecution also introduces the crime scene photos, physical evidence, and Perry's confession. The defense only is able to put forth character witnesses and makes closing arguments — more against the death penalty than for the innocence of the murderers. But both Dick and Perry are found guilty and sentenced to death. Mrs. Meier grieves after the verdict; she is joined in her grief by the squirrel that will not take food from her, but continues to wait for Perry.
The two men arrive at death row, where they are to stay for a total of five years. During this time, Dick and Perry live with other prisoners who are on death row. The inmates are all within speaking distance to each other, but their cells line up so they cannot see one another. Perry attempts to starve himself to death, though his motivation may have been to be declared legally insane. The other occupants of death row are introduced, among them is Lowell Lee Andrews, a large and highly intelligent young man who killed his entire family and feels no guilt or grief. Eventually, young soldiers George Ronald York and James Douglas Latham arrive on death row. These two men are good looking and pleasant, despite having gone on a multi-state killing spree because of their belief that the world has become hateful.
The title of the chapter is revealed: On death row, the term used for those who have gone to the gallows and been executed is, "gone to The Corner."
Dick finds an attorney to appeal his conviction based on what he considers his lack of a fair trial. He is ultimately unsuccessful.
Andrews is put to death on November 30, 1962. Dick and Perry are put to death on April 14, 1965. Al Dewey attends the execution and feels deep, true empathy for Perry in his last minutes. Dewey sees Perry as a child.
The final scene of the book jumps ahead and finds Susan Kidwell and Al Dewey meeting one another in a graveyard. Susan is attending college and living in New York, just as she and Nancy had planned. The book ends optimistically, looking ahead to the future, and with a feeling that Susan and Al are moving on with life.
Perry's position as the occupant of the woman's cell contributes to his emasculation, which has been happening throughout the book. Considering the way Dick used to call Perry pet names like "Honey" and Perry's noted small stature, his placement in a holding cell meant for women seems natural.
Perry's earns the affection of Mrs. Meier, who cooks for him and gives him books to read. Perry almost becomes a member of the Meier family, and he accepts the love and care of Mrs. Meier in a way he could never achieve with his own mother or sister. Mrs. Meijer knows what Perry did and she is disturbed by it, but she also cannot help but love and care for him — and to grieve for Perry when he is gone. This is the unconditional love from a family member that Perry has yearned for his whole life, but has now come too late. Perry's desire to give comfort to Mrs. Hickock by changing his statement to try to clear Dick of the murders was Perry's method of forgiving womankind, now that he has met a woman who treats him with compassion.
In Perry's writings, he notes how much he misses Dick, which once again alludes to the intensity of their relationship. At one point, Perry writes about seeing Dick's father passing by his cell door. Perry calls out to him, but when Dick's father doesn't respond, Perry concludes that it "Could be he never heard me." Perry's inability to figure out the feelings of other people is illustrated through his responses to moments like this.
Perry continues to dismiss those around him, including the doctors who examine him for signs of mental illness. He believes that they wanted to be "entertained," which is enough for Perry to discredit them. He could also be referring to the journalists, witnesses, courtroom attendees, local townspeople, Don Cullivan, and the readers of the book itself. To be curious, to want to know the truth, is both human and at the lowest point of humanity. The blood lust that drove Dick and Perry to commit murder is the same one that makes other people want to know the details of said crimes. Capote is guilty of this need to be both informed and entertained by the murders, and he includes Perry's opinion of the doctors as of means of acknowledging the reader's true reason for opening this book.
Perry's true nature and motivation continue to be revealed as he references his sister, for a second time, as someone he wishes had been in the house the night of the murders. This confirms that Perry's actions were misplaced rage against those who either mistreated him, or failed to protect him, during his youth. This includes the woman at one of the boy's homes he was forced to live in — who abused him for wetting the bed. In a written statement, Perry wishes that he could have hurt the people who mistreated him or made fun of him. Perry's writings reveal that his home life differed strongly from Dick's. Unlike Perry, Dick had parents who never fought, who stayed together, and gave him everything they could. Perry, although the guiltier of the two men, remains the more sympathetic character. Perry's desire to hurt people is brought on by the emotional abuse he suffered as a child. It is not enough, as Al Dewey said, to make one forgive Perry for his misdeeds, but it is enough to garner some compassion for Perry as opposed to Dick, who has no reason to cheat, steal, and hurt people. Dick also further dehumanizes himself as he admits to having committed pedophilic acts, and via his previously unspoken motivation for invading the Clutter home, which was to rape Nancy.
The true nature of the people of Holcomb comes through in Mrs. Hickock's tribute to them. She asserts that no one had been unkind to her, pointing out that the waitress at the diner would regularly give her ice cream on her pie without charge. This indicates that, despite the paranoia and grief that befell the town, there is not a lynch mob mentality or any sensation of rage directed towards either the suspects or their families. Instead, the people of Holcomb recognize that there is enough sadness and regret to go around, but everyone is entitled to kindness and understanding. That the Clutters were known especially for their kindness and generosity magnifies the tragedy, and further demonstrates how unimaginable this crime was to these people.
Perry repeats his motivation for committing the murders several times, but he sometimes alters it. Sometimes, Perry is motivated by showing Dick was he is capable of; other times he is motivated by his rage towards his family and caregivers. In truth, Perry's motivation to kill the Clutters seems to remain a mystery to him. He wonders aloud to Don Culliver why he did it, and he admits that Dick didn't do it. While reporters, investigators, doctors, and the court finally get the answers they seek, Perry never does. And his lack of self awareness and insight makes Perry a tragic figure. Yes, Perry harbors resentment about his childhood, but he has no real self-pity and he never alludes to his upbringing as cause for his actions, only for his own personal pain and deep desire to be liked, to be loved.
The lengthy sections regarding the psychological analysis of Perry as well as other killers who do not have clear motives for their crimes reflect Capote's effort to leave no rock unturned. The legal opinions, personal writings, and extensive interviews of the killers do not completely suffice to bring a conclusion to the story, or as close as one can get in such a case. But the introduction of scientific evidence and psychological theories brings about both authenticity and a sense of finality to a writing that is both nonfiction and literary. Capote makes a case not only for the cause of the murders, but also for the existence of a new book genre. The final line in the section, which tries to explain this kind of violence, supports this assertion: "So it would appear that by independent paths, both the professional and the amateur analyst reached conclusions not dissimilar."
After Dick and Perry are convicted and sent to death row to await their fate, Capote reintroduces them as "the Clutter murderers." In the early stages of the book, Capote refers to them as "the two men," then later as "Dick and Perry." But once they are convicted, Capote refers to them as "the Clutter murderers" — with only "Clutter" being capitalized. The passages immediately following their arrival on death row is peppered with morbid and dark imagery: "Coffin-shaped edifice"; "black as widow's veil"; "doomed"; "scream." These words help portray a place with no hope, and a place that reminds one of death and misery.
By introducing Lowell Lee Andrews, Capote compares this new killer to Perry. Like Perry, Andrews created a separate identity, that of a gangster, instead of accepting himself as he was. Perry's most evident alter ego is that of an educated person. But the arrival of Andrews creates an environment where Perry is no longer able to indulge in his fantasy. He is no longer the most well-read or the most educated of his peers. Andrews even corrects Perry's speech, the way Perry used to correct Dick's. When Andrews is executed, he leaves behind a poem for Dick. Dick is able to believe that Elegy Written in a Country Churchyard could have been written by Andrews, but Perry purports to have been the poet.
Perry feels, at times, that he is living "deep underwater," which harkens back to his initial desire to go skin diving and find buried treasure. He also sleeps all day and is quoted as saying, "I pretend I'm a tiny little baby that can't keep its eyes open." He says the phrase "tiny little baby" in a voice so child-like that it creates a moment of compassion, seeing Perry as both a child and someone who once was a tiny little baby, and who wants only to start over as something innocent.
In the company of Lowell Lee Andrews, George Ronald York and James Douglas Latham, Dick and Perry become ordinary. Their crimes pale in comparison to George and James' killing spree, and their cold-heartedness does not measure up to that of Andrews, whose victims were his own family. The "Clutter killers" are now part of a community, and they are not even the most significant members. The context in which they live throughout the book continues to define them more than their own actions.
Continuing with his writing style of foreshadowing and offering revelations after the fact, Capote indicates the death of the two men by Alvin Dewey reading about it in the paper. The impression is that Dewey had stopped being so intimately involved with the killings, and as a result he didn't even realize that they had been executed. However, the next section begins, "Dewey had watched them die," revealing that he is still deeply connected with the case and did know about the executions before reading about them in the paper. Capote now forces us to witness, along with Dewey, every moment, just as with the killings, of Perry and Dick's execution. Capote initially spares the reader the gory details, but then suddenly reveals them on the page, without warning. It is this literary style that acts with brutality rather than information. And it creates a sensation not unlike being assaulted.