Plot summary
During a tapir hunt in the Mesoamerican jungle, Jaguar Paw (Rudy Youngblood), his father Flint Sky (Morris Birdyellowhead), and their fellow tribesmen encounter a procession of traumatized and fearful refugees. The procession's leader explains that their lands have been ravaged, and with Flint Sky's permission, the procession passes through the forest. When Jaguar Paw and his tribesmen return to their village, Flint Sky tells his son not to let the procession's fearful state seep into him. At night, the tribe's elder tells the village a fable of man dangerously never filling his want, despite having the capabilities of the world's animals. The villagers follow the story with music and dance, leaving Jaguar Paw to ponder.
The next morning, after Jaguar Paw wakes from a nightmare, something terrible happens in reality too: with everyone still sleeping, Jaguar Paw sees strangers enter the village, setting aflame homes with their torches. The raiders, led by Zero Wolf (Raoul Trujillo), attack the villagers in their dawn raid and subdue as many as possible. Jaguar Paw slips out of the village with his pregnant wife Seven (Dalia Hernández) and his little son Turtle Run, lowering them on a vine into a small cave (a chultun, shaped something like a well)[9] to hide them. Jaguar Paw returns to his village to fight against the raiders, but he is subdued with the rest of his tribesmen. A raider whom Jaguar Paw attacked, Middle Eye (Gerardo Taracena), prepares to execute Flint Sky in front of his son. Flint Sky tells Jaguar Paw not to be afraid, and Middle Eye slits Flint Sky's throat.
Before the raiders leave the village with their prisoners in shackles, one suspicious raider severs the vine leading into the ground cave, trapping Jaguar Paw's wife and son within. The raiders and their captives make a trek toward a Mayan city, encountering failed maize crops and slaves producing plaster. They also pass a small girl with smallpox who warns the raiders that their end is near. In the city's outskirts, the female villagers are sold as slaves, and the male villagers are escorted into the city to the top of a step pyramid. A priest sacrifices several captives by pulling out their hearts and then decapitating them. When Jaguar Paw is on the altar to be sacrificed, a solar eclipse stays the priest's hand. The priest declares the sun god Kukulkan satisfied with the sacrifices, and he asks the sun god to restore light. The eclipse passes, and light returns to the world.
Zero Wolf, told to dispose of the captives by the priest, takes them to a ball field. Their captives are released in pairs to run the length of the field while the raiders target them with javelins, arrows, and stones. Jaguar Paw successfully reaches the field's end and though injured by an arrow piercing, bypasses a raider "finisher", Zero Wolf's son Cut Rock, by killing him. An enraged Zero Wolf pursues Jaguar Paw into the jungle with his fellow raiders. The chase leads back to the forest in which Jaguar Paw's village was located, and Jaguar Paw declares from the bottom of a waterfall up to the raiders that they are in his territory now.
Zero Wolf's raiders fall to both the forest's elements and Jaguar Paw's traps. The clouds begin to rain, which begin to flood the ground cave in which Jaguar Paw's wife and son are still trapped. Jaguar Paw kills Zero Wolf by setting off a trap meant for hunting tapir, and he is chased by two remaining raiders out to a beach. There, they encounter conquistadors and missionaries making their way toward the shore in rowboats (the Spanish conquest of Yucatan actually started in 1519). The amazement of the raiders allows Jaguar Paw to flee. He returns into the forest to rescue his wife and son from the cave. He finds that his wife has given a submerged birth to a healthy second son, and the family is rescued. Jaguar Paw leads them deeper into the forest, leaving behind the conquistadors anchored in ships off the beach.