Glanton's company continues through the freezing cold past the ruins of the old hacienda at San Bernardino, where they kill some old bulls that charge at them. One of the bulls impales James Miller’s horse with its horns, and Miller shoots the bull in the head. After that, Glanton’s company rides on, following the Santa Cruz River until they pass the old mission at San Jose de Tumacacori. The judge lectures Glanton’s men on the history and architecture of the mission, but most of them doubt that he's ever been there before. The men follow the judge into the church, where a dying man lies on the floor.
Company member John Prewett reveals that he shot the man, and he tells the others that there is another hermit hiding in the church. The first man dies and the gang waits outside the church while John Jackson locates the other hermit. The hermit speaks German, so only the judge can communicate with him. The judge determines that this hermit is the dead man's brother, and observes that both men have lost their minds out in the wilderness. As the company moves on, the hermit yells after them, still not fully aware that his brother is dead. Glanton confesses to the judge that he hates seeing white men lose their minds.
The gang continues to track the Apaches. Further out in the desert, the company discovers the bodies of their missing scouts, skewered and hanging from a tree. They had clearly been tortured as their heads are roasted, and their tongues have been torn out. Glanton’s men cut the bodies down and leave them on the ground.
That night, they ride through the mission of San Xavier del Bac and past the ruins of several haciendas to arrive at the outskirts of Tucson. They finally find the Apaches camped along the South Wall. The Apache leader is a small, dark man, who happens to be carrying one of the dead scouts' weapons. When the Apaches approach the company, though, Glanton’s horse bites off the Apache leader’s horse’s ear. Glanton slaps his horse as punishment, but the Apaches are already deadlocked with Glanton’s men. The leader rants about his horse, and the judge tries to placate him by saying it was an accident. Then, another group of riders emerges from behind the wall. Their leader, Mangas, doesn’t seem concerned about the horse’s ear; he simply asks the judge where they have come from. Mangas commands all the Apache men to step away from the Americans, and they follow his orders. Mangas then negotiates with Glanton. If Glanton brings them some whiskey from Tucson, they will repay him in gold and forgive the horse incident. They all agree to meet in the same place three days later.
Glanton’s company arrives in Tucson, where they are greeted by an American named Couts who is leading a small garrison stationed in the city. Couts explains that his garrison returned to Tucson only four days earlier to find it under informal Apache rule. Couts and his men are drunk, and they explain that they expected the Apaches to withdraw once the liquor ran out. At a local bar, Glanton asks the proprietor where he can find recruits to join his gang for a trip to California. The barkeep directs them towards a man whom he knows will join them. The man, called “the owner," is accompanied by a mentally disabled man, “the idiot,” whom he keeps in a cage and charges people to see. Glanton tells the owner that he will bring both of them to California for a hundred dollars, less if the owner can recruit some other men.
Later, Glanton's company heads to an eating-house. The proprietor, Owens, asks them to sit separately from the white patrons because of John Jackson (who is black). David Brown hands Owens a gun and dares him to shoot Jackson, who then stands and pulls his own gun. Before Owens can make a move, Jackson shoots him in the head. The company quickly moves to a nearby cantina, and they are still there when the police arrive to arrest Owens's killer. Glanton denies any culpability, and the judge backs up his claim. The lieutenant leaves because he is unable to do anything. The owner (of the idiot) starts drinking whiskey with Glanton's men, and he decides to charge more to exhibit the idiot in California. He also reveals that the idiot is his brother. That evening, the lieutenant returns to investigate Owens's murder further, but the judge explains jurisprudence to him so effectively that the lieutenant does not act on any of the allegations.
The next morning, Glanton's gang hears that a young Mexican girl has been kidnapped. A day-long vigil descends into debauched chaos and by midnight, Glanton’s men are naked and drunk, pounding on doors and demanding drink and women. They ride out of Tucson at dusk the next day. At this point, the group is comprised of 21 men, a dog, a flatbed holding the idiot in his cage, and a whiskey keg for Mangas and his men. The company meets up with Mangas to make the exchange, and they then ride up the hills into the west.
Two days later, Glanton’s company encounters a legion from Sonora led by Col. Garcia. Col. Garcia's men are looking for a band of Apaches, even though they are worn down and unarmed. They try to greet Glanton's company, but Glanton pushes by without acknowledging them.
That night, Glanton's company gathers around the fire to discuss some grand themes: the moon, the stars, and the potential existence of other life forms in the universe. The judge claims that all existence has its own order, and no man can understand it because man’s own mind is part of nature. The judge performs a magic trick with a gold coin; he throws it into the darkness, and it returns like a boomerang. Thinking this is an illusion, the other men try to find the coin in the woods when the sun comes up, but they can’t find it and conclude that the magic is real.
As the company keeps riding, they encounter more scenes of death and destruction: dead horses, abandoned saddles, and even crude crosses marking impromptu graves. The judge continues espousing his philosophies, this time about war. The judge believes that war has always been a part of human life, and that it is the primary trade of all the men in Glanton’s company. He claims that war is the truest form of divination, even equating war with God. Later, when the judge finds a huge femur bone in a water tank, he gives Glanton's men a lesson in paleontology. Three days later, the company reaches the Colorado River. There is a ferry that will take them across the river for a dollar a head. There are also some Yuma Indians camped near the river, who have eaten all their horses for sustenance. The company sets up camp on a nearby hill.
A doctor named Lincoln, who is from New York, runs the ferry. Glanton brings Dr. Lincoln to the area where his company is camped, and the judge speaks to the doctor intently. That evening, Glanton and five others ride down to the river to speak with the Yuma leader, a man named Caballo en Pelo. Overnight, Glanton and Caballo en Pelo devise a plan to seize the ferry from Dr. Lincoln.
When Glanton's small group returns to camp, a group of local women have crowded around the idiot's cage; they are furious with his entrapment. The owner, who reveals that the idiot’s name is James Robert, hands the caged man over to a woman named Cloyce Bell. The other women torch the cage, and together, they clean the idiot and tuck him into real blankets. That night, the idiot runs away from the women. Later, the judge discovers him in the water and returns him to camp.
Dr. Lincoln visits with Glanton, David Brown, Irving, and the judge. When the judge warns Dr. Lincoln to fortify himself against the Yumas, the doctor confesses his trust in them, which Glanton then mocks. Glanton receives Dr. Lincoln's permission to fortify the hill and charge his Howitzer cannon.
Two days later, as Glanton has planned, the Yumas attack the river crossing. However, David Brown and Long Webster use the cannon to kill over a dozen Indians, which was clearly not part of their agreement. Chaos ensues as Glanton and his men charge thorough the injured Yumas, killing people and taking their scalps. The next day, the ferry belongs to Glanton and Glanton alone. He raises the crossing charge, but after a while gives up the façade and begins robbing potential passengers outright and sending them destitute into the desert. Dr. Lincoln tries to reason with Glanton, who simply pays him his share of the revenue and sends him back to his quarters. Lincoln never comes out again.
The next month, a company from Kentucky, led by General Patterson, approaches the Colorado River and refuses to bargain with Glanton. Instead, Patterson’s company constructs their own ferry downriver, which the Yumas manage. General Patterson’s ferry operator is a man named Clanaghan, whose headless body soon comes floating downriver.
One morning, after a night of heavy drinking in San Diego, David Brown finds himself in a squatting house made of hides; he can’t remember anything from the night before. His companions (Toadvine and Long Webster) and their mules are tied up at the grocers’. Brown demands their return, but the alcalde (Mexican policeman) sends Brown away. Brown then brings a brand-new rifle to the local blacksmith and asks him to cut the barrels down. The man refuses, not understanding why anyone would want to ruin such a beautiful gun. When Brown threatens the blacksmith, he leaves to fetch the sergeant, and they return to find Brown sawing the gun himself. Brown reiterates his threat.
On his way back to town, Brown finds that Toadvine and Long Webster have been released. The three of them watch the ocean for a while, and then spend the afternoon drinking. As usual, they start a fight in the bar. In the process, Brown sets a young soldier on fire. The next morning, Brown wakes up in a prison cell with another soldier guarding him. He tries to bribe the young man to let him out but to no avail.
Meanwhile, Toadvine and Long Webster return to camp without their mules, any provisions, or David Brown. Upon hearing their story, Glanton takes some of his men to San Diego, where they hang the alcalde from the ceiling and beat him until he releases Brown. Brown, without knowing any of this, finds himself free two days later. When he leaves the prison, Brown kills his young guard, taking all his effects and cutting off his ears as souvenirs.
Toadvine, Long Webster, and David Brown head to the gold fields while Glanton returns to Yuma to drink alone. Dr. Lincoln has emerged from his hut, dirty and disheveled. He begs Glanton to help him and points towards the judge, who is standing naked on the hill with John Jackson beside him. Glanton pushes the doctor away.
The next day, the ferry stands idle while Glanton’s men engage in drunken revelry. At one point, Jackson is urinating in the river when an arrow pierces him through the heart. The Yumas, led by Caballo en Pelo, swarm the American fortifications. Their first move is to behead Dr. Lincoln before awakening the rest of Glanton’s drunken men. Caballo en Pelo splits Glanton’s head open with an axe. The Yumas burst into the judge’s quarters, where they find him consorting with the 12 year old girl and the idiot. The judge also has the Howitzer in his tent - he fires it at them and then escapes into the woods. The Yumas raise up Glanton’s body at throw it into the fire, with his (still living) dog tied to it. They have killed eight people in total. The kid and Toadvine remain upriver, however, and have to fend off four Yumas on their own. The kid's leg is pierced by an arrow during the fight.
The kid and Toadvine end up alone in the desert, and their water soon runs out. The kid takes the lead by shooting one of the Yumas from his hiding place; he is a great shot. At Alamo Mucho, Toadvine and the kid find Tobin. The three of them hide from the circling Yumas in the well. After the kid fires at three Yumas, the Indians finally retreat. The next morning, the bedraggled threesome comes upon the judge and the idiot running naked through the desert. The judge buys Toadvine’s hat to protect himself from the sun, and he invites the three men to share his meat. Tobin hisses at the kid to kill the judge because at this moment, the judge is naked and unarmed. The kid can’t do it. Therefore, Toadvine stays behind with the judge and the idiot, while the kid and Tobin move on towards California. On their way out, they meet David Brown riding east on horseback. They inform him of all the deaths and tell him where to find the judge. Brown rides on.
The next day, the kid is drinking some water when the judge and the idiot appear. The judge fires at Tobin and the kid, so they hide. Tobin argues that the kid should fire at the idiot, but he misses his chance. The kid's leg wound is now badly infected. The judge calls out to the kid, offering him water if the boy reveals himself. He doesn’t budge. Then, the kid sees Tobin walking towards him, holding a cross made of skins. The judge shoots Tobin in the neck. Even though the ex-priest miraculously survives, his wound is severe. He hisses at the kid to shoot one of the judge’s horses. The kid manages to shoot one of the horses in the chest and the other one dead-on. The kid then attempts to escape despite his injured leg, but then, he hears the judge asking him to throw down his gun. The judge promises that he will not hold the kid responsible for the betrayal or the attack; he knows that the kid acted as he did only because of Tobin's influence.
The kid sneaks back to Tobin, however, and they escape despite their injuries. When they think they have traveled a safe distance, they go to sleep. When they awaken, though, they see the Judge and the idiot following them through the desert.
In this section, McCarthy delves deeper into the camaraderie between Glanton’s men. Even though they are as a group dehumanized and violent, there is a moral code that unites them. For example, after Jackson kills Owens, Glanton could easily have betrayed Jackson for his own safety. In fact, he could have forced Jackson to sit alone away from the white customers so as not to cause any problems, but instead he defends Jackson's right to eat with his men. This shows that even though Glanton is a cold-blooded killer, he does have a sense of loyalty - even through it masquerades as pride. McCarthy hints at Glanton's humanity earlier in the novel as well, when Glanton insists that his men join him at Angel Trias's home to celebrate their successful scalping mission. Glanton once again acts out of loyalty when he sets out to free David Brown, who has been imprisoned in town. At one point, the reader learns that Glanton even has a wife and child that he will never see again.
While these glimmers of decency make Glanton a more nuanced and sympathetic character, they are also ironically pessimistic. If Glanton were purely evil through and through, he would be too far removed from most readers' understanding of humanity and therefore, would fail to strike an emotional chord. However, by making Glanton seem vulnerable, McCarthy forces readers to relate to him. As a result, we then have to consider our own dark sides and propensity for cruelty. Therefore, McCarthy's characterization of Glanton underlines his point that man is essentially violent.
Another conflict that emerges in this section is between those who work inside the organized system (i.e., the army) and those who work outside of it (i.e., Glanton's gang). Even when these groups have similar goals, power and ego fuel clashes between them. For example, when David Brown is imprisoned in San Diego, a young solider is assigned to guard him. This young man is also an American and he supposedly shares the same goal as Glanton's gang: they all want to defeat the Apaches in the name of American expansion. However, the soldier's decision to work within the system costs him his life. He has a stricter moral code that keeps him from becoming an outlaw like David Brown. Meanwhile, the young man's murder is symbolic, not personal; Brown kills his guard in a show of opposition to the system. Brown does not have the foresight to see that he and this boy ultimately want the same thing, he just considers him an obstacle to his own freedom.
This section also marks Glanton's downfall; his greed and ego prove to be his undoing. He does not consider the consequences of his actions because he believes that the Yumas are inevitably weaker than him; Glanton's arrogance is ultimately what allows Caballo en Pelo to catch him completely off guard. McCarthy expresses Glanton's hubris through his writing style, particularly when he describes Callaghan's death; the author uses one sentence to describe the moment when the Yumas see their operator’s headless body floating in the river, which mirrors the thoughtless and simplistic thought process that went into Glanton's decision to murder the man. Glanton's flagrant inherent disinterest in the implications of his own violent act explains how the Yumas are able to mount a coordinated attack right under Glanton's nose.
Once Glanton is gone, the bonds of camaraderie within his company become tenuous. The connections that do remain strong are somewhat surprising; for example, judge and the idiot stick together, as do Tobin and the kid. Strangely, the kid still has a deep respect for the judge and refuses to kill him. Everyone else - like Tobin and Toadvine - understand how dangerous the judge is and they are frightened to be under his control.
Meanwhile, the judge becomes attached to the idiot, even though nobody else (including the idiot's brother) ever pays him much attention. This could perhaps be because like the judge, the idiot cannot help but be himself and act on his most basic instincts. To his brother, the idiot was merely a sideshow and/or a burden; the women who try to "rescue" him looked at him with pity. The judge, however, does not ask anything of the idiot; both men are free to act on their most despicable and natural urges. The judge's fondness for the idiot also mirrors his attraction to children - the judge clearly enjoys taking charge of innocents.
Finally, it is important to note the metaphysical and Biblical content of the judge's many speeches. He struts around naked again in this section, which is representative of the purity of his expression (even though his ideas are rather terrifying at times). After Glanton's death, the judge's pursuit of the kid and Tobin, as well as his constant offer of sustenance, has devilish implications. Judge Holden is not a charitable man; rather, he wants Tobin and the kid to be beholden to him and to owe him their lives. Therefore, to refuse his offer is to refuse to acknowledge his power, which is a terrible offense in the judge's eyes.