Chapter 1
Writing as an adult, Antonio Márez recounts events that occur when he was six years old. Ultima, an elderly curandera, or healer, comes to live with his family. The night before Ultima's arrival, Antonio lies in his bed in the little attic above his mother's kitchen. He hears his parents talking about Ultima. His father, Gabriel, says that Ultima is old, and though she has served the people as a healer her entire life, she has now been reduced to living alone out on the llano, the great New Mexico grassland near Antonio's home. Antonio knows that his father is a vaquero, a cowboy, and loves the wildness of the llano, while his mother, María, is from the Luna family, who are all farmers, and prefers civilization. Long ago, María convinced Gabriel to move to the town of Guadalupe so that their children could have an education, and Gabriel still misses the life on the open plains of the llano.

Antonio is happy that his parents have decided to take Ultima into their home and to provide for her. As he drifts off into sleep, he has a dream in which he floats over the hills of the llano to the village of Las Pasturas and toward the window of a lighted hut. There, a woman is in labor, and Antonio recognizes that he is witnessing his own birth. After the baby Antonio is born, his mother's brothers arrive and declare that he will be a Luna and perhaps become a priest. His father's brothers declare that he will continue their tradition of restless wandering on the llano. Each family wishes to dispose of the afterbirth according to their family traditions: the Lunas seek to bury it in the earth, while the vaqueros seek to burn it and scatter the ashes across the open plains. Ultima halts the ensuing disagreement by stating that she will bury the afterbirth herself. She declares that only she will know Antonio's destiny.

Antonio is anxious the next morning. He knows that he will soon begin school, and he is nervous at the thought of leaving his mother. He talks with his mother about his birth; she confirms that Ultima helped at her bedside, and she urges her children to treat Ultima with respect when the elderly woman arrives. She then strongly implies that she wants Antonio to become a priest. Troubled, Antonio decides to visit his friend Jasón but finds that he is not home. Antonio surmises that Jasón has defied his father's wishes by going to visit an Indian who lives alone in the hills. Antonio returns home to work in the garden.

Later that day, Gabriel arrives with Ultima. When Antonio shakes Ultima's hand, he senses the power of a whirlwind pass around him. He calls her by her given name instead of the customary salutation, Grande, and Ultima says that she knew when he was born that she would one day be close to him. Ultima's owl takes up residence near Antonio's home. Although owls are said to be a disguise taken by brujas, or witches, Antonio dreams that the owl carries the Virgin of Guadalupe and all the babes of Limbo to heaven.

Chapter 2
The whole family is glad that Ultima has come to stay with them. Mária is happy to have a woman to talk to, and Antonio's two older sisters are happy to have someone to help with their chores so that they can spend more time playing together with dolls. Gabriel talks to Ultima about his desire to move to California, a wish he now feels will never come true because his older sons are fighting in World War II, and he cannot move his young family alone.

Antonio is happy because he and Ultima quickly become friends. Ultima takes Antonio on walks to gather herbs and teaches him about their healing properties. Antonio says that he begins to hear the voice of the river. He senses that his family's peaceful isolation is about to end. Jasón's father, Chávez, comes to the Márez home shouting that Lupito, a local war veteran, shot Chávez's brother, the sheriff, dead. When Gabriel joins Chávez and the other men searching for Lupito, Antonio secretly follows them to the river. He sees Lupito, armed with a pistol, hidden in the water. Antonio makes a small noise, and Lupito looks down at him. But just then, the searchlights fall on Lupito, and he is confronted by his pursuers. Lupito runs off again into the reeds, out of sight of the men on the bridge. Gabriel and Narciso, the town drunk, try to explain to the mob that Lupito is shell-shocked because of the war, but after crying out something about Japanese soldiers, Lupito shoots his pistol into the air, drawing the fire of his pursuers. Lupito begs Antonio for his blessing as he dies.

Antonio runs home, sobbing and reciting the Act of Contrition, the last prayer that Catholics say before dying. When he realizes that Ultima's owl has been with him the whole time, he loses his fear. He fears that the river will be stained with blood forever. He thinks about the town, which he knows his father despises, and the llano, and he wonders why Lupito had to die. He remembers when his father built their house. Rather than choosing to build on a patch of fertile ground, Gabriel built a house on a barren place at the start of the llano. Antonio enters the house and Ultima meets him. She cleans him and puts him to bed. Ultima explains that it is not for them to judge whether Lupito or the men who killed him will go to hell. Antonio dreams of his three older brothers discussing their father's dream to build a castle in the hills. When Antonio states that they must gather around their father, they reply that he is supposed to fulfill María's dream and become a priest. When they try to cross the River of the Carp to build Gabriel's castle, a mournful voice calls Antonio's name. His brothers shrink in fear, saying that it is La Llorona, the "Weeping Woman," or Lupito asking for his blessing. Antonio declares that it is the presence of the river. He calms it so that his brothers can cross.

Chapter 3
When Antonio wakes, he ponders the fate of Lupito's soul and those of the men who killed him. He thinks that, according to Catholic principles, Lupito must be in hell because Lupito died having committed a mortal sin. He hopes that God will forgive Lupito, but he thinks sadly that God does not forgive anyone. He wonders whether the water of the river will carry Lupito's soul away.

Antonio lies in bed and listens to his parents quarrel. Their frequent Sunday morning arguments about religion are a result of Gabriel's Saturday night drinking. María is a devout Catholic, but Gabriel's vaquero mindset causes him to distrust priests because to him they stand for order and civilization. Antonio knows that Gabriel's father once dragged a priest from church and beat him after the priest preached against something that Antonio's grandfather had done. At last Antonio goes downstairs, and María scolds Antonio for not being properly formal when greeting Ultima. Ultima requests that María not scold Antonio, as the night was hard on all the men in town. María protests that Antonio is still a baby. She says that she thinks it is a sin for boys to become men. Gabriel hotly declares that it is not a sin, only the way of the world, and María argues that life corrupts the innocence and purity that God bequeaths to children. She says bitterly that if Antonio becomes a priest, he will be spared from the corruption of life. Gabriel pours coffee for Ultima, and Antonio realizes with some surprise that Gabriel and Ultima are the only grown-ups he knows who eat or drink before taking Communion on Sundays.

Many women in town are dressed in mourning because they have lost sons and husbands in the war. Antonio notes that the war has indirectly claimed two more victims: Chávez's brother and Lupito. Antonio lingers near his mother, who smoothes his hair, and he feels soothed by her presence. He feels another jolt of anxiety when he realizes again that when he starts school soon, he will have to leave her. Antonio and Ultima discuss the events of the previous night. Antonio asks Ultima how his father can take Communion if he committed the sin of firing at Lupito. Ultima replies that she doesn't think Gabriel fired at Lupito, but she warns that no one should presume to decide whom God does and does not forgive. On the way to the church, the family passes a brothel situated in a ramshackle mansion that belongs to a woman named Rosie. María makes her children bow their heads as they pass, and Antonio realizes that Rosie is evil, but evil in a different way from a witch. Before mass, Antonio mingles with the other boys. As they play, they discuss the night's events. One of the boys brags that his father saw Lupito kill the sheriff. Antonio says nothing about Lupito's death.

Chapter 4
As the summer comes to an end, Antonio spends his mornings walking with Ultima, gathering herbs and medicines from the llano. During this happy time, Antonio grows to love both the llano and the river. Ultima teaches him that plants have spirits like people and tells him stories about the old days. Antonio realizes that Ultima is happiest when she is out on the llano, and her happiness helps him to realize that he too is a part of the llano and a part of nature. Antonio tells Ultima that he will soon visit his mother's brothers, and Ultima tells him that she is an old friend of his mother's father. He asks her why his Luna relatives are so quiet, and she replies that it is in the Luna blood to be quiet like the moon, just as it is in the Márez blood to be loud and restless like the sea. (In Spanish, la luna means "moon" and el mar means "sea.") Antonio feels the presence of the river and wonders again about Lupito's soul.

Back at home, Antonio and Ultima dry the plants on the chicken shed. María tells them over dinner that, as Antonio had expected, it will soon be time to visit the Lunas to help with the harvest, a yearly ritual that keeps Antonio close to his grandfather and uncles. Antonio spends the rest of the afternoon playing at Jáson's house and then cuts wild alfalfa by the river to feed to the rabbits.

Every night, Antonio's family prays before María's statue of the Virgin of Guadalupe, a beautiful, two-foot-tall likeness of the Virgin in a blue gown. Antonio loves her because she always forgives; the Virgin is his favorite saint. He knows that she is the patron saint of his land. On the foot of the statue a little paint has chipped away so that the white plaster is visible, and Antonio thinks of the plaster as the Virgin's pure soul.

That night, Antonio hears Ultima's owl singing its mournful song outside his attic window. Antonio slips into sleep and has a dream in which the Virgin speaks to María. The Virgin promises María that his older brothers will return home from the war safely. When María asks her to make Antonio a priest, Antonio sees the Virgin wearing the clothing of mourning for him while standing on the moon. When he cries out in his sleep, Ultima comes to comfort him.

Chapter 5
Pedro Luna, Antonio's uncle, takes Antonio, his mother, his sisters, and Ultima to the Luna farms to help with the harvest. They stop first at the home of María's father, Prudencio Luna. Afterward, they settle into the home of one of María's brothers, Juan Luna, because it is his turn to host his sister and her children. Antonio overhears Juan urge María to send Antonio to them for a summer before Antonio is "lost" like his older brothers.
Chapter 6
That fall, Antonio begins school. When Ultima blesses him, he again feels a whirlwind sweeping around him. He recalls the evil whirlwinds on the llano, which he has been taught to ward off with the sign of the cross, and wonders why he feels the same whirlwind in Ultima's presence. Reflecting on this similarity, Antonio wonders if the powers of good and evil are the same. María presses Ultima to name Antonio's fate. Ultima replies sadly that Antonio will be "a man of learning." In his first day, Antonio learns to write his name, much to his teacher's pleasure. However, the class first laughs at him because he cannot speak English and because he eats green chili in tortillas for lunch. Feeling like an outcast, Antonio begins eating lunch with other children whose language and customs are different.
Chapter 7
The war ends, and Antonio dreams of three giants, his brothers. They ask for his "saving hand" because they are dying. Antonio wakes just in time to greet his brothers upon their return.
Chapter 8
Antonio's brothers spend the winter sleeping all day and spending their money on women and drink. All three of them suffer trauma from the war. Their parents say that they have "war-sickness." In the spring, the brothers are restless to build their own independent lives, resisting Gabriel's urgings to follow his old dream of moving to California with them.
Chapter 9
Antonio dreams that his three brothers urge him to enter Rosie's brothel. Antonio calls out that he must resist because he might become a priest. His brothers León and Eugene predict that he will eventually enter the brothel. Antonio begs Andrew to stay outside. Andrew promises not to enter until Antonio loses his innocence. Antonio hears the voices of a priest and María, who say that innocence lasts only until understanding. Antonio hears Ultima call out that his innocence is in the lonely llano. Antonio awakes to hear his brothers arguing with their parents. The brothers want to leave the family and strike out on their own. León and Eugene leave the next morning, but Andrew stays behind.

Andrew walks Antonio to school. The Vitamin Kid beats them in a race, calling Antonio a giant killer. At the end of the year, Antonio's teacher, Miss Maestas, promotes him from first to third grade. After school, Antonio goes fishing with Samuel, the Vitamin Kid's brother. Samuel asks if Antonio has ever fished for carp. Antonio replies that he hasn't because to do so is bad luck. Samuel tells Antonio a story that Jasón's Indian originally told. The story says that the gods sent the first people to the valley but forbade them to eat the carp. During a terrible drought, the people disobeyed the rule. One god pleaded for mercy, so the gods turned the people into carp instead of killing them. The god who saved the people grew sad, so he became a carp as well. However, he is larger than the other carp and golden in color. The story explains why eating carp is a sin. Samuel says that Cico, a local boy, will take Antonio to see the golden carp. When Antonio returns home, María is angry that he is so late. When she learns of his double promotion, however, she quickly forgets it.

Chapter 10
When María's youngest brother, Lucas Luna, is near death that summer after having fallen ill the previous winter, neither a Las Vegas doctor nor the local priest can cure him. When Pedro, Lucas's brother, asks for Ultima's help, he explains that Lucas saw the daughters of Tenorio Trementina dancing the Black Mass, a blasphemous satanic ritual. When Lucas challenged them with a cross made from two sticks, they fled the scene. Within the week, Lucas fell ill.

Ultima says that she will need Antonio's help to cure Lucas. Antonio states that he will be proud to assist a curandera. As they approach El Puerto, they see the horned day moon, the moon of the Lunas, between two dark mesas at the end of the valley. When Ultima arrives in El Puerto, she forbids the Lunas to kill the coyotes that will surround Prudencio's home when she works her cure. When Ultima takes Antonio to confront Tenorio to warn him that his daughters must lift the curse or suffer the consequences, Tenorio makes the sign of the cross. Ultima declares that his daughters gathered Lucas's hair for their curse after he came to Tenorio for a haircut. Tenorio denies her accusations and calls her a bruja, or witch.

Ultima closes herself and Antonio in Lucas's room. After she forces a mixture of kerosene, water, and herbs down Lucas's throat, she asks Antonio if he is afraid, and Antonio says that he is not. She explains that the reason for his courage is that good is always stronger than evil. Antonio hears Ultima's owl attacking the coyotes surrounding Prudencio's home. Antonio enters a trance and finds that he cannot move or speak. When Lucas writhes in pain, Antonio feels pain as well. Ultima makes three clay dolls covered with wax and forces Lucas to take more medicine. Afterward, Antonio drifts to sleep. When he wakes, he vomits green bile. Ultima catches it in rags that she stores in a bag. Afterward, Antonio is able to keep down some atole, a gruel made of corn meal. Lucas screams in pain, vomiting a squirming mass of hair. When Lucas successfully eats a bowl of atole, Ultima declares the cure finished. The house fills with happy people, but some whisper the words bruja and hechicera (meaning "witch" or "sorceress"). Ultima burns the mass of hair and dirty linen in the grove where Lucas challenged Tenorio's daughters.

Chapter 11
Cico offers to take Antonio to see the golden carp. After confirming that Antonio has never fished for a carp, Cico asks Antonio if he believes the golden carp is a god. Crestfallen, Antonio replies that he cannot believe in any god except the god of his church because he is a Catholic. At Cico's request, Antonio swears by the cross that he will never hunt or kill a carp. Afterward, Cico and Antonio visit Narciso's garden, where they eat carrots. Cico explains that Narciso's magic and an underground spring make the garden so lush. Narciso plants by the light of the moon.

Antonio's group of friends invites Antonio and Cico to play ball. Ernie claims that there is a witch living in Antonio's house. Horse asks Antonio to do a magic trick for them. Angry at Ernie's taunting, Antonio agrees. He vomits the carrot juice on the ground, frightening his friends. Cico and Antonio run to a hidden pond where the huge, beautiful golden carp makes its appearance. Cico explains that the carp lives in the Hidden Lakes, a place with a strange power like the presence of the river, but stronger and hungrier. A mermaid lives there, trying to lure men to their deaths. Cico warns Antonio never to go there alone.

Cico explains that the golden carp prophesied that the weight of people's sin would cause the land to sink and be swallowed by the underground lake beneath it. When Antonio replies that it is not fair to the men who don't sin, Cico tells him that all men sin. The story saddens Antonio, and he feels burdened by the knowledge. When he returns home, he learns that Ultima already knows about the golden carp. She tells Antonio that he must find his own truths in adulthood. That night Antonio dreams about the conflicting beliefs he has encountered, as well as the conflict between his parents' wishes for him. Ultima tells Antonio and his parents that the water of the moon and the sea are the same water and that each family member is part of the same cycle.

Chapter 12
Antonio notices three wax-covered clay dolls on Ultima's shelf. One seems to be bent over in pain. Ultima forbids him to touch the dolls and warns him to stay away from Tenorio. She gives him an amulet containing dried herbs to protect him from danger. One evening, Narciso bursts into the Márez home to report that one of Tenorio's daughters has died. Tenorio told everyone that he found Ultima's little pouch of herbs under his daughter's bed. Narciso warns Ultima that Tenorio is coming with a drunken lynch mob hungry for a witch's death. At that moment, Tenorio and his cohorts arrive. With Antonio at his side, Gabriel demands that they identify themselves and state their business.

To guard against witches, one man has thrust through his lips needles that have been blessed by a priest. Narciso declares that they can pin the needles over Gabriel's door in the sign of a cross. If Ultima is a witch, she cannot walk through the door. The mob agrees to abide by the test. Ultima's owl suddenly gouges out one of Tenorio's eyes. When everyone looks up, Ultima has passed through the door. The mob disperses, but Tenorio vows to kill Ultima. Antonio notices that the needles are no longer pinned above the door. He never finds out if they simply fell or if someone had broken the cross.

Chapter 13
Gabriel accompanies his family to El Puerto and stays to take part in the Lunas' harvest for the first time. Antonio ponders the conflicting belief systems of the Catholic Church and the golden carp. He wishes there were a god that always forgave and never punished. He wonders if God is too much like a man. Antonio asks Pedro why he and Antonio's other uncles did not come to warn Ultima like Narciso did. Pedro admits that he was a coward, but he vows to stand by Ultima from now on. Antonio's uncle, Mateo, reports that the surviving Trementina sisters have woven a cottonwood coffin for their dead sister because a witch cannot be buried in a pine, cedar, or piñon coffin. He describes the frightful ceremony for a Black Mass funeral. Antonio has a dream in which Mateo's description of the ceremony is enacted, but when he looks inside the coffin, he finds Ultima. He awakes just in time to see the El Puerto priest refuse to give the dead woman the funeral mass and, therefore, burial in hallowed ground. The whole town witnesses their public shame. Tenorio will never again be able to sway the townspeople to join his vendetta for revenge.
Chapter 14
Antonio returns to school in the fall. Samuel is pleased that Antonio saw the golden carp. He warns Antonio that their classmates will not understand his family's defense of Ultima. When Antonio arrives at the schoolyard, Ernie tries to pick a fight by saying Antonio has a witch in his house. He also shouts that Andrew visits Rosie's house regularly. Antonio ignores the charge against Andrew, but he stands up for Ultima. He and Ernie get into a fight, and before long, everybody is fighting in a pile. The teachers separate the boys, but no one is punished. No one teases Antonio about Ultima afterward.

On the day that Antonio's class is scheduled to give a Christmas play at school, a fierce blizzard covers the ground with snow. Antonio and his rambunctious friends are the only students in their class who show up to school. Their teacher, Miss Violet, decides to have them perform the play in front of the rest of the school anyway. The boys practice all morning, but some of them are not happy at playing the girls' parts. The play becomes a hilarious farce.

Walking home morosely, Antonio sees Tenorio, the saloon-keeper, and Narciso, the town drunk, fighting in the street. Another of Tenorio's daughters is sick. Before stumbling away, Tenorio vows to kill Ultima. Narciso rushes off to find Andrew, one of Antonio's older brothers. Antonio follows Narciso to Rosie's house. To Antonio's horror, Narciso knocks on the door and asks for Andrew. Antonio wonders if the fact that Narciso is looking for Andrew at the brothel means that Andrew has already lost his innocence. When Andrew refuses to take Narciso seriously and warn his parents of Tenorio's threat, Narciso trudges into the blizzard to do it himself. Antonio stays out of sight and follows him.

Antonio hears a pistol shot ring out. He finds Tenorio and Narciso fighting under a juniper tree. When Antonio screams, Tenorio aims at him, but his pistol refuses to fire. After Tenorio flees, Antonio hears Narciso's last confession. He stumbles home to report what he has seen. Antonio falls into a deep fever and dreams that he begs God and the Virgin to forgive Andrew and Narciso. The Virgin replies that she will not forgive Narciso if Antonio does not ask her to forgive Tenorio as well. Antonio cries out for Tenorio to be punished, but God declares that he cannot be a god who is all-giving while taking vengeance on Tenorio at the same time. Antonio cries for God to forgive his own sins.

In his dream, Antonio sees the blood of Lupito and Narciso mix in the river. A mob gathers, calling for Ultima's blood. Antonio's brothers beg him to bless and forgive them. However, they turn into the Trementina sisters when Antonio approaches them. They cut Antonio's hair and mix it with a toad's entrails and a bat's blood. Afterward, they drink it, and Antonio dies despite his mother's prayers and Ultima's magic. Antonio is sentenced to purgatory because he died without taking the Eucharist. Lead by the sisters, a mob kills Ultima, Antonio's family, and Antonio's friends. Afterward, the mob catches and eats carp. A great hole opens in the ground, and water rises out of it, but the sinners take no heed. The sun turns red, and the sinners' skin falls off. When there is no one left alive in Guadalupe, the farmers from El Puerto come to gather the ashes of Antonio and his family. They bury the remains in the holy ground of their fields. The skies clear, and the golden carp swallows everything, good and evil. He ascends to the heavens to become a new sun, shining over a new world.