The kid is born in Tennessee in 1833, but by the age of fourteen he already has “a taste for mindless violence” and runs away from home. By 1849, he rides into the town of Nacogdoches. There, the kid encounters a giant charismatic man named Judge Holden who incites a crowd to violence against a preacher. The kid also meets Louis Toadvine. Toadvine and the kid fight at first, only to work together a day later in burning down a hotel. As the kid rides out of Nacogdoches, past the fire he’s helped to start, the Judge smiles at him.
The kid rides his mule over the prairie, where he meets a hermit who shows him a black man’s shriveled heart. After more days on the trail, the kid arrives in Bexar, also in Texas, where he goes to a cantina to work in exchange for a drink but ends up brutalizing the bartender. A soldier named Sergeant Trammel, serving under Captain White, finds the kid at a river and tells him that the Captain was impressed by how badly the bartender in Bexar was beaten. What’s more, he wants to recruit the man who did it into his army. After an interview with Captain White himself, who is intent on reclaiming Mexican territories for the U.S. (against U.S. policy), the kid enlists.
Despite a Mennonite’s warning that they’ll awake God’s wrath, Captain White’s army of filibusters (people engaging in unauthorized warfare against a foreign country) ride into Mexico, through barren, hostile terrain. Within days they are set upon by a war party of Comanche Indians and massacred—only eight filibusters escape, including the kid, Captain White, and a man named Sproule whose arm is badly wounded. The kid and Sproule set out through the desert together. After a wagon carries them to a town, Sproule dies, and the kid is placed under arrest by Mexican soldiers, presumably for being part of Captain White’s army. The soldiers lead the kid through town, past a jar with Captain White’s head floating in it. Then, over the next few days, they escort him and other prisoners to Chihuahua City.
In the prison in Chihuahua City, the kid meets up with Toadvine, also incarcerated, along with a Kentuckian called Grannyrat. Toadvine soon arranges for the three of them to be released from prison to join a gang of scalp hunters, newly arrived in the city, in whose company rides none other than the Judge. The gang’s leader is a dark-haired, small man named Captain John Joel Glanton.
After arming themselves, the gang sets out, first for the town of Janos where Glanton takes the gang’s first scalp, then north. At camp one night, one member of the gang, the black Jackson, kills another, the white Jackson, who had told him not to sit with the white men around their campfire. Later, while riding, the gang is ambushed by Apaches, but manage to ward them off and take a scalp. Some nights later, the gang camps with a group of squatters, and around the campfire the Judge delivers the first of his many lectures, this one on how nature is the word of God.
Some nights later, a member of the gang, an ex-priest named Tobin, explains to the kid how the gang came to ride with the Judge, whom they found sitting on a rock in the desert. He helped them to manufacture gunpowder from natural resources which they used to massacre the Apaches pursuing them; the Judge has been Glanton’s second-in-command ever since.
One night, as the scalp hunters camp amid the ruins of the Anasazi, an ancient Native American people, the Judge sketches the artifacts he finds and claims that all people exist as representations in the minds of others. He also tells a story which suggests that the children of both bad and ideal fathers are doomed to lives of desperation and emptiness.
A little more than two weeks pass before the gang discovers and massacres a village of Gileños, a group of Indians. None are left alive, the dead are scalped, but Glanton is disappointed to learn that Gomez, the leader of the Apaches on whose scalp is placed a very high price, was not in the village. Nonetheless, the gang rides back to Chihuahua City to receive payment for the scalps they took. They are welcomed as heroes, paid handsomely with gold, and banquet drunkenly and debauchedly for several nights before riding out of the city on August 15.
The gang goes on to massacre a band of peaceful Tigua Indians, and even ride into a mountain village where they murder Mexican villagers after an altercation at a cantina as well as Mexican soldiers. They take the scalps even of these non-Indians; but though the gang manages to exchange the Tigua and even Mexican scalps to the Chihuahuan government for gold, their crimes soon come to light, their contract with the Chihuahuan government is rescinded, and a sizable bounty is posted on Glanton’s head.
In response, the gang rides to Sonora, another Mexican state, and the government there also contracts them to hunt the Apaches and take scalps. After massacring a village on the Nacozari River, however, the gang encounters an army of Sonoran cavalry led by General Elias. The Sonorans must have become aware of the gang’s acts of savagery, or the bounty on Glanton’s head, because Elias’s army skirmishes with the gang, then pursues them north. During the firefight, some of the gang members are wounded, and the kid is left behind to kill one of them, Dick Shelby. However, and despite personal risk, the kid decides to let Shelby live. After many brutal days and nights of trekking thereafter, the kid reunites with the gang, who have burnt and discarded the scalps taken on the Nacozari.
The gang members who have survived Elias’s pursuit ride into Santa Cruz, then into Tucson, Arizona. There black Jackson murders the proprietor of a restaurant, but the Judge manages to have any charges against him dropped. There the gang also meets a man named Cloyce Bell who owns and exhibits in a cage his intellectually disabled brother, James Robert Bell, more often referred to as "the idiot." The gang agrees to escort the Bell brothers to California for a fee.
The gangs end up riding to the Colorado River. On the way the Judge lectures on how warfare is eternal, the ultimate trade. “War is God,” he concludes. At the Colorado River, the gang meets Dr. Lincoln, who runs a ferry there. The gang also meets a band of Yuma Indians, with whom Glanton conspires to seize the ferry. However, when the Yumas advance on the ferry, Glanton violently betrays them so that the gang can appropriate the ferry for itself. When the Yumas attempt to operate another ferry downriver, Glanton’s men murder the rival ferry operator. The gang quickly grows rich exploiting and robbing their passengers. However, the Yumas in time organize a counterattack against the gang, which results in the death of most of its members, including the black Jackson and Glanton himself.
Among the surviving gang members are the kid and Tobin, both seriously wounded, along with Toadvine, the Judge, and the "idiot." These men are scattered in the desert but eventually meet back up with one another at a well. The Judge attempts to buy the only pistol among them, that belonging to the kid, but the kid refuses. Tobin advises the kid to kill the Judge, whom he fears will kill them all, but the kid declines this also.
Tobin and the kid set off together. However, they are soon pursued by the Judge, now dressed in Toadvine’s clothing as well as that of David Brown, one of Glanton’s former deputies (not present during the Yuma massacre) who found the Judge in the desert. The Judge is also armed with Brown’s rifle and has the "idiot" on a leash. After several encounters with the Judge, the kid and Tobin escape him and make it to San Diego, where Tobin goes to find a doctor and the kid is jailed. The kid is visited by the Judge in jail, who tells him that he would have loved him like a son had he not poisoned the gang’s enterprise by having some mercy in his heart for those the gang murdered. After this visit, the kid tells a corporal in charge of the jail where the gang has hidden gold in the mountain. He is released soon after and provided medical attention.
After recovering, the kid goes to Los Angeles, where he witnesses the public execution of Toadvine and Brown. He spends his subsequent years doing various jobs and traveling. By 1878, at the age of forty-five, he finds himself in a saloon in Fort Griffin, Texas. There, after so many years, he meets the Judge one last time. The Judge informs the kid (now referred to as the man) that the two of them are the last survivors of Glanton’s gang, and he lectures on fate, will, and rituals. The kid tells the Judge, “I aint with you,” and parts ways with him. However, when he enters the saloon outhouse that same night, the Judge is waiting for him and takes him into his “immense and terrible flesh,” presumably murdering him. The Judge then takes to the dance floor, where he dances and fiddles expertly before the men and prostitutes assembled, announcing that he never sleeps and will never die.
Blood Meridian concludes with an epilogue, in which an anonymous man makes holes in the earth and uses a steel instrument to strike fire in them, behind whom people mechanically follow.