The novel opens by describing Ts’its’tsi’nako, the Thought-Woman, who is telling this entire story. Stories are the only way to fight off illness and death and stand up to evil. The story begins with sunrise.
Tayo, a Pueblo man, wakes up in his spare ranch house, dreaming deliriously of different scenes from his life. One memory in particular bothers Tayo – he was unable to execute a Japanese soldier in the Philippines during World War II because he saw his Uncle Josiah in the Japanese uniform. The ranch where Tayo lives in New Mexico, unlike the wet Philippines, is suffering from a drought that came because, Tayo believes, he prayed for the rain to stop while he was in the jungle during the war. Tayo tells a story about Corn Woman scolding her sister, Reed Woman, who then takes the rain away in her anger. Tayo thinks back to his return from the Veteran’s Hospital in Los Angeles where he felt like a white spirit and couldn’t keep any food down.
Tayo’s friend Harley, a fellow war vet, comes riding on a burro and convinces Tayo to ride with him to the nearest bar, even though Tayo doesn’t like to drink. As they ride the burro, Tayo thinks about his cousin Rocky, who joined the army with Tayo but died overseas. Thinking of Rocky makes Tayo fall off the donkey and throw up.
The story moves back to the time just after Tayo return home from the Veteran’s Hospital. Auntie takes care of Tayo instead of sending him back to the Veteran’s Hospital, but Tayo knows that Auntie resents him as much as ever for his mixed blood. Grandmother wants to call a medicine man to cure Tayo’s illness, but Auntie thinks that a medicine man won’t be able to help Tayo because Tayo is not full-blood Pueblo. Grandmother stops Auntie complaining about Little Sister (Tayo’s mother) sleeping with white men, and calls the medicine man Ku’oosh anyway. Ku’oosh comes to Tayo’s sickbed, speaking only the native Laguna language, and tells Tayo that the world is fragile. Tayo realizes that he must do something to restore the damage the war has done to the world. When Ku’oosh leaves, Tayo is finally able to keep a meal in his stomach. Tayo gradually gets better and starts to help Auntie’s husband, Robert, with the ranch work.
Tayo goes out drinking one night with some other war veterans to numb his pain. The other veterans, Emo, Harley, and Leroy, tell stories about the white women that they had sex with while on leave during war time. Tayo, agitated by these stories, begins to rant about the loss of respect that Native Americans face once more but the other men only want to relive their glory days. Tayo flashes back to his capture by Japanese soldiers. He carried Rocky, even though Rocky was already dead, but the Japanese soldiers forced him to leave Rocky’s body behind and took Tayo to a prison camp.
The novel returns to Tayo’s present, as Harley picks him up from the ditch where Tayo ended up after the night drinking. Tayo notices how dusty the land is due to the drought, and remembers Uncle Josiah telling him how droughts happen when people forget their duty to the land they come from. The novel switches to a story about a town that became so obsessed with doing magic that they stopped caring for their mother corn altar. The Corn Mother, angered by their neglect, takes all rainclouds away from the town.
Returning to Tayo and Harley, the two men finally make it to the bar. While Tayo drinks a beer, he remembers a time when he went deer hunting with Rocky. Tayo paid respect to the deer for its death, but Rocky pays no attention to these old rituals. Rocky was a star student and football player at their boarding school in Albuquerque, and believed that he had to give up the old ways to be a success. Harley breaks into Tayo’s thoughts, reminding Tayo of the last time they went to a bar and Tayo almost killed Emo.
Tayo remembers that night night. Emo begins raving about how they all deserve to take white women as payment for everything that white people have stolen from Native Americans. Then Emo insults Tayo for being half white. Emo takes out a bag of teeth that he says came from Japanese prisoners of war. Tayo, drunk and enraged, breaks a beer bottle on the table and stabs Emo in the stomach.
The novel flashes back to Tayo and Rocky enlisting in the army. As they sign up together, Rocky calls Tayo brother for the first time. As children, Auntie made sure that Tayo and Rocky were not close friends, constantly reminding Tayo that his white blood keeps him from being part of the family. Tayo thinks that Auntie gave up on helping Little Sister, Tayo’s mother, because Auntie’s Christian morals separate her from the native community. In the Corn Woman story, Hummingbird tells the people about a ceremony that will help them bring the rain back. The ceremony creates a fly. This fly goes with Hummingbird to the fourth world to talk to the Corn Mother.
Auntie is angry that Tayo wants to join the army with Rocky instead of staying to help Josiah care for the ranch. Josiah has recently bought new cattle, a special hybrid breed that he says will be able to survive a drought. Josiah goes to Cubero to visit the woman who helped him buy the cows, a Mexican dancer named Night Swan. Josiah fell in love with Night Swan and visited her often before the cattle took over his free time. Auntie believes a drought will come as punishment for Josiah sleeping with a Mexican. Tayo tries to do all the old rituals meant to bring back rain, still believing in the old stories. The next day, storm clouds gather and Josiah sends Tayo to Night Swan to tell her that Josiah won’t be able to visit because of the rain. Night Swan invites Tayo in, sleeps with him, and tells Tayo that she has been watching him because of his green eyes.
In Corn Woman’s story, Corn Mother tells Hummingbird and Fly to get Old Buzzard to purify the town so that she can send rain again. Buzzard tells Fly and Hummingbird to get tobacco to give him as an offering. Tayo thinks back to when he visited Gallup with Robert, where homeless people from every ethnicity live under the bridges. Tayo himself lived under a bridge with his mother for the first four years of his life, watching the other hopeless children and avoiding his mother when she brought men back to their hut. When Rocky and Tayo enlisted, they threw coins off the bridge in Gallup. Rocky wished for a safe return, but Tayo didn’t wish at all. Standing on the bridge with Robert after coming back from the war, Tayo finally wishes for a safe return.
Seeing that Ku’oosh’s rituals only partially helped Tayo, Grandmother and Auntie send Tayo to Betonie, a medicine man in Gallup. Betonie lives in a hogan near the poorest part of the city, and has green eyes like Tayo. Betonie tells Tayo that his illness will only be healed when he does his part to help heal the world, a new ceremony that will help put right the wrongs that white men do to the land. Betonie tells a story about a boy who lived with bears and had to be carefully called back to his life with humans. Betonie leads Tayo through a ceremony that will bring him back to life, a ceremony that includes Mexican and white power as well as Native traditions.
In the Corn Mother story, Fly and Hummingbird go back to Corn Mother to ask where to get tobacco. She sends them to caterpillar. In Tayo’s present, Betonie sends Tayo on a journey to find his uncle’s cattle and heal the drought. Tayo heads off on foot, but Harley and Leroy soon see him and pick him up. A Native American woman named Helen Jean is with them and they all go to a bar. Helen Jean leaves the Native American men in favor of some Mexican men. Harley, Leroy, and Tayo get kicked out of the bar when Harley starts a fight. Tayo leaves Harley and Leroy behind to continue Betonie’s quest on horseback.
As he searches for the cattle, Tayo meets a woman who invites him in to her house to rest on his journey. In the Corn Mother story, the caterpillar gives Hummingbird and Fly tobacco. Tayo sleeps with the woman that night, then has a dream about his uncle’s cattle. The next morning, Tayo follows a barbed wire fence until he sees his uncle’s cattle in the distance, then cuts a hole in the fence to herd the cows through later. He stops for the night and sees a mountain lion pass by, then puts yellow pollen in the mountain lion tracks.
The next morning, Tayo sets off at a fast gallop, but some white men catch up to him. Tayo falls off his horse and hits his head. The men hold him at gunpoint until they are distracted by mountain lion prints and leave Tayo in favor of hunting the mountain lion for its pelt. Tayo falls unconscious. When he wakes again, it is snowing. Tayo hears someone chanting a traditional Laguna hunting song – it is a hunter. The Hunter takes Tayo back to his house, which turns out to also be the house of the woman he slept with earlier. The man is her brother. And the woman has Uncle Josiah’s cattle with her near the house.
That spring, Robert and Tayo go get the cattle from the woman’s house. Tayo takes care of the cattle all spring on his uncle’s ranch, noticing how much healthier and peaceful he feels. One day, the woman returns to visit Tayo and finally tells him her name: Ts’eh. Ts’eh asks Tayo to gather a specific plant for her if she isn’t there to do it herself.
That fall, Ts’eh has to leave and Tayo returns to town to finish his healing ceremony with the other veterans. Harley and Leroy see him on the road and pick him up again. They have been drinking heavily and convince Tayo to drink too. Tayo blacks out in the truck, then wakes to find Harley gone. Tayo grabs a screwdriver and follows Harley and Leroy’s footprints. Tayo goes into an abandoned uranium mine, thinking of the atomic bomb that caused so much destruction. While he is inside the mine, he sees Emo and some other veterans drag Harley into the mine and start to torture him for letting Tayo get away from the truck. Tayo is sick at Emo’s evil actions, and wants to use the screwdriver to murder Emo. Yet Tayo is able to get control of the witchery’s influence on him and choose not to add more evil to the world.
Tayo leaves the mine and gathers the last plant for Ts’eh, then begins to travel back to his Aunt’s house. The Corn Mother story ends as Hummingbird and Fly give Old Buzzard tobacco to purify the town. The storm clouds return and Corn Mother warns the people not to get distracted with magic anymore. Tayo tells Ku’oosh and the other men his whole story and Ku’oosh says that Ts’eh is the Reed Woman who will bring back the rain. Harley and Leroy are found dead and Emo later escapes to California. Grandmother wonders at the end of this story, thinking that she has heard the story before with different names. The novel ends with a sunrise.