While on a quest to hunt tapir deep in the Mesoamerican jungle, Jaguar Paw (Rudy Youngblood), along with his father Flint Sky (Morris Birdyellowhead) and their tribe, stumbles upon a somber caravan of refugees. Their leader describes the devastation of their lands and seeks passage through the jungle. Flint Sky advises his son to remain strong and not let the refugees' despair affect him.
The following morning, after dreaming of the refugee leader, Jaguar Paw awakens to chaos as warriors invade their village, setting huts ablaze. The attackers, commanded by Zero Wolf (Raoul Trujillo), capture the villagers. In a desperate bid, Jaguar Paw manages to escape with his pregnant wife Seven (Dalia Hernández) and their young son Turtles Run (Carlos Emilio Báez), lowering them into a deep cave using vines. As he fights back against the raiders, he manages to kill one, but quickly finds himself overpowered. In a heartbreaking moment, a raider named Middle Eye (Gerardo Taracena), who narrowly survived Jaguar Paw's attack, brutally kills Flint Sky right before his eyes.
Before departing with their captives, one of the raider captains, Snake Ink, observes the vines hanging from the cave, growing suspicious. He severes them, thus trapping Seven and Turtles Run inside the cave. The prisoners are taken into the jungle, where they soon encounter another group of marauders who have also captured refugees. During their journey, Cocoa Leaf, a wounded captive bound with Jaguar Paw, nearly falls off a cliff, but with great effort, they manage to pull him back. However, Middle Eye callously executes Cocoa Leaf by letting him fall.
As they journey towards a Mayan city, the group witnesses the destruction of forests and failed crops, alongside villages devastated by a plague. A dying girl predicts doom, declaring that a solar eclipse will lead a man with a jaguar to destruction. Upon reaching the city outskirts, the male captives, including Jaguar Paw's friend Curl Nose (Amílcar Ramírez), are led to a step pyramid where a high priest conducts savage sacrifices by ripping out hearts and beheading victims in the name of their god, Kukulkan.
Just as Jaguar Paw is about to be sacrificed, an eclipse descends, causing panic among the spectators. The high priest interprets it as a sign of divine satisfaction and orders that the remaining captives be 'disposed of.' Next, they are brought to a ball court, where captives must run for their lives against the raiders, with the faint promise of freedom lingering before them. Jaguar Paw observes as his friends are brutally killed, and during his turn, he sustains an arrow wound but continues. With the aid of a dying comrade, he manages to escape and flees into the jungle.
While pursued by Zero Wolf and his men, Jaguar Paw finds himself in peril, yet he cleverly navigates through hazardous terrains, even surviving an encounter with a fierce black jaguar. As he continues his escape, he confronts his relentless pursuers using strategy, deploying nature’s elements, ultimately leading to a climactic showdown.
After precarious encounters, he confronts Zero Wolf and, in a final twist, outsmarts him with a hunter's trap, killing him. In the end, as the residual chaos subsides, Jaguar Paw stumbles upon the presence of conquistadors arriving by ships, giving him a fleeting moment of hope. Reuniting with Seven, who has just given birth to their second son, Jaguar Paw reflects on their future. As they observe the foreign ships, Seven suggests they approach, but Jaguar Paw resolutely decides they should return to the safety of the forest for a fresh start.
