The narrator explains that the tale that follows is the origin story of the ancient Quiché and Mayan world, though this version has been secretly recorded during Spanish rule. The narrator and their fellow scribes are recording the story because there's no longer a place to see the original Mayan text.
In the beginning, there's only sky and sea. Three gods—Hurricane, Newborn Thunderbolt, and Sudden Thunderbolt—descend from the sky and address Sovereign Plumed Serpent, a god who lives in the sea. They decide to empty the sea to create land, and also decide that they must then create humans so that there's someone to praise the gods' work. Land suddenly rises out of the water, and Sovereign Plumed Serpent creates animals. When all this is done, the gods ask the animals to praise their creators—but the animals only make unintelligible noises. The gods condemn the animals to be food for future humans. Next, the gods attempt to create a human out of mud, but the mud human melts. After this setback, the gods approach Xmucane and Xpiayacoc for advice about carving humans out of wood. Xmucane supports creating wood people, and they miraculously spring to life. However, the gods are again disappointed, as the wood people forget their creators. Hurricane brings a flood down on them, and the wood people turn into monkeys.
Because the sun has not yet risen, everything is still dark. Despite this, a god named Seven Macaw decides to impersonate the sun and moon so he can give light to the wood people. He decorates his face with turquoise and precious metals that reflect light and create the illusion of sunlight. The twin boy gods, Hunahpu and Xbalanque, understand that Seven Macaw and his sons, Zipacna and Earthquake, are evil, as they all "magnify themselves." One day, the boys hide under Seven Macaw's tree and shoot him in the jaw with their blowguns. When Seven Macaw falls and Hunahpu runs to pick him up, Seven Macaw rips Hunahpu's arm off and flees with it. Xbalanque and Hunahpu enlist the help of Great White Peccary and Great White Coati, suggesting that the two pose as grandparents and bonesetters to trick Seven Macaw. When the four walk past Seven Macaw's house later that day, Seven Macaw is yelling in pain. He inquires with the "grandparents" as to what they're doing, and when they explain they're bonesetters and dentists, Seven Macaw pleads for help. The grandparents simply pluck out Seven Macaw's turquoise teeth and his precious metals. Seven Macaw dies of shame, and Great White Peccary and Great White Coati reset Hunahpu's arm.
Hunahpu and Xbalanque next turn their attention to Zipacna. One day, as Zipacna bathes, a group of gods called the Four Hundred Boys drag a log to their hut. Though Zipacna offers to help the Boys, his strength worries them. They invite him into their hut, but Zipacna declines the Boys' hospitality. The Boys decide to trick Zipacna and kill him, so the next day they ask Zipacna to help them dig a deep hole. When Zipacna is at the bottom of the hole, the Boys throw a huge log down after him—but Zipacna, a skilled trickster himself, takes shelter in a side tunnel he dug. Three days later, Zipacna escapes his prison and kills the Four Hundred Boys by destroying their hut. When Hunahpu and Xbalanque learn of this, they build a fake crab and sneakily starve Zipacna for two days. When they lead Zipacna to the crab, which is tucked under a mountain, Zipacna wiggles into the space and the mountain comes to rest on his chest. He turns to stone.
Next, Hurricane instructs the twins to make Earthquake sit down in the east. When the twins find Earthquake destroying mountains, they tell him about a massive mountain in the east. Earthquake is thrilled to be able to bring down such a huge mountain and follows Hunahpu and Xbalanque, who shoot birds along the way. When they stop to rest, the twins coat one bird in plaster and decide that it will be for Earthquake. Earthquake eats the bird, soon loses strength, and the twins bury him.
The narrator goes back in time to tell the story of Hunahpu and Xbalanque's father and uncle, One Hunahpu and Seven Hunahpu. They spend their time playing a ball game with One Hunahpu's sons, One Monkey and One Artisan. The ball game is disruptive to the lords of Xibalba (the underworld), so the high lords One Death and Seven Death summon One and Seven Hunahpu to play ball with them. One and Seven Hunahpu agree. On the way to Xibalba, One and Seven Hunahpu reach the Crossroads. They follow Black Road until they reach the council place of the Xibalban lords, where they greet the lords—though the first two seated "lords" are actually just wooden manikins. The lords laugh and send their guests to a house called Dark House. One and Seven Hunahpu are instructed to keep two cigars and a torch lit overnight, but they fail at this task.
In the morning, the Xibalban lords kill their guests. They decapitate One Hunahpu and place his head in a tree, which soon bears fruit. A young maiden, Blood Moon, approaches the tree. One Hunahpu spits in her hand and she becomes pregnant with Hunahpu and Xbalanque. When Blood Moon’s father, Blood Gatherer, realizes she's pregnant, he instructs the owl messengers to cut out her heart. The messengers instead help Blood Moon escape Xibalba, and bring back a "heart" made of tree sap for the lords. Blood Moon approaches Xmucane—who is One Hunahpu’s mother—for help, though Xmucane is wracked with grief and doesn't believe Blood Moon's story about her pregnancy. Xmucane sends Blood Moon to gather corn as a test, and Blood Moon passes by making many ears of corn out of corn silk.
When Xbalanque and Hunahpu are born, their older brothers, One Monkey and One Artisan, are resentful. They try to kill their little brothers, but the twins thrive anyway. One day, Hunahpu and Xbalanque ask their older brothers for help retrieving birds out of a tree. When One Monkey and One Artisan climb the tree, the tree grows, traps them in it, and the brothers turn into monkeys. Later, Hunahpu and Xbalanque try to call their monkey brothers with music, but Xmucane's laughter scares the monkeys away.
Xbalanque and Hunahpu assure their grandmother Xmucane that they'll take care of things, and so they take over gardening duties. Their tools cultivate the land magically, though when the twins return to their garden the next day, they find that the trees and bushes have reclaimed the land. When the twins keep watch that night, they see all the animals singing for the land to reclaim the garden. The boys capture a rat, who tells Hunahpu and Xbalanque that their father's ball playing equipment is hidden in Xmucane's house, and they make a plan to retrieve it. Hunahpu and Xbalanque send their grandmother away while the rat cuts down the equipment, and from then on, the boys spend their days playing. The noise bothers the Xibalban lords, and they summon the twins to play in Xibalba. Xmucane receives the summons, and she sends a louse to carry her message to her grandsons. Hunahpu and Xbalanque agree to accept the summons, but they plant two ears of corn in Xmucane's house to act as a signal for whether they're alive or dead.
When Xbalanque and Hunahpu reach the Crossroads, they send a mosquito ahead to bite all the lords and learn their names. Thus, the twins are able to greet all the lords by name. One and Seven Death send the twins to Dark House with the lit cigars and torch, and Hunahpu and Xbalanque make their items appear lit by using macaw feathers and fireflies.
In the morning, the lords are perplexed but they play ball anyway. When a knife flies out of the Xibalbans' ball, Hunahpu and Xbalanque threaten to leave, and the lords agree to use a regular ball. The lords ask that if they win, the twins should bring them bowls of flower petals as a prize. The boys agree and allow themselves to lose. The Xibalbans send the boys to other trick houses for the night, and the boys employ cutter ants to raid the Xibalbans' garden. When Hunahpu and Xbalanque present the petals in the morning, the lords look pained. The rest of the day proceeds with a ball game and another trick house that night, where a snatch-bat bites off Hunahpu's head. Xbalanque fashions a new head for his brother out of a squash, and in the morning they again play ball. Xbalanque tricks the lords and Hunahpu reclaims his head, and the twins win the match. The twins know that they must die, however, so they summon two seers and tell them to grind the boys' bones and scatter them in the river.
The next day, One Death tries to engage Hunahpu and Xbalanque in a game of jumping over a large oven, but the boys jump right in and die. The seers do as they were told and five days later, Hunahpu and Xbalanque crawl out of the river as vagabonds. They perform great tricks that attract the attention of One Death and Seven Death, and the lords summon the “vagabonds” to perform for them. During the performance, Hunahpu and Xbalanque sacrifice One and Seven Death—but the Xibalban lords don't come back to life. The twins then attempt to reassemble their father and uncle, but decide to leave them buried. Finally, the twins enter the sky as the moon and sun, and the Four Hundred Boys become the stars.
Going back in time again, Sovereign Plumed Serpent and Xmucane grind corn to create the first four humans: Jaguar Quitze, Jaguar Night, Not Right Now, and Dark Jaguar. These men are too perfect, however, and the gods decide to partially blind them so that the humans can't become divine. The gods create wives for the men, and humans flourish. The humans travel and establish citadels. At their second citadel, the humans are given the gods Tohil, Auilix, and Hacauitz to worship. Not long after, the first sunrise comes. The gods turn to stone, and the humans give thanks. Soon, Tohil instructs his followers that the neighboring tribes will begin hunting him. The first four men begin offering animal sacrifices to Tohil, who turns into a real boy.
The men start hunting and killing the tribes, and the tribes devise a trap to kill Tohil. They send Wailing Woman and Lust Woman to tempt the boy gods, but the gods send the women home with enchanted cloaks. When one of the tribal lords dons a cloak decorated with wasps, the wasps come alive and sting the lord. After this, the tribes decide to attack. Tohil instructs the four men on how to set a trap using manikins, stolen armor, and wasps, and the trap is successful. Even the men's wives can kill the tribes, and the tribal people who survive become vassals. After this victory, the first four men disappear, leaving their sons a Bundle of Flames. The sons treat the bundle as a memorial to their fathers.
From then on, the Mayan people flourish. They engage in war and experience prosperous times, and the Quiché house becomes the most powerful. The narrator lists the most important people from several family lines, and explains that the Quiché lords become great through devotion and through studying the Council Book. Finally, the narrator declares that this is the end, as there's no longer a place to see the people or the book now that the Castilians have invaded.