It is the early 16th century, somewhere in the Central American jungle. A tapir runs frantically through the forest before it springs a trip wire trap and is impaled on a swinging branch full of spikes. Young Jaguar Paw (Rudy Youngblood
) puts the tapir out of its misery and eagerly divides its internal organs between his fellow hunters; Curl Nose (Amilcar Ramírez
), Smoke Frog (Israel Contreras
), and Cocoa Leaf (Israel Ríos
). Blunted (Jonathan Brewer
) receives the tapir's testicles as the brunt of a joke since he and his wife have yet to have any children. Jaguar Paw's father, Flint Sky (Morris Birdyellowhead
) offers some remedial help, giving Blunted some red leaves that he instructs him to use the next time he and his wife try.
They are soon interrupted by a band of refugees passing through the forest, looking downtrodden. One of them, a fisherman (Hiram Soto
), addresses Jaguar Paw and explains that their village was attacked and that they are seeking a new beginning. They exchange food before the group moves on, though Jaguar Paw is keen to know more about what happened. His father silences him and they return to their village. Just before they get back, Flint Sky explains to his son that the refugees were infected with fear and that it should not be brought into the village to fester.
Jaguar Paw goes to his hut and admires his small son, Turtles Run (Carlos Emilio Báez
), before greeting his very pregnant wife, Seven (Dalia Hernández
). Blunted returns to his wife, Sky Flower (Iazua Larios
), whose mother (María Isabel Díaz
) impatiently tells him to hurry and give her grandchildren. Moments after entering their hut, Blunted runs out screaming and holding his privates before seating himself in a water trough. Flint Sky falls to the ground laughing, as the leaves he gave Blunted were meant to cause a burning sensation when rubbed. Blunted yells at him but starts laughing with everyone else. That night, an old storyteller (Espiridion Acosta Cache
) tells how man once received gifts from the forest until the forest had nothing left to give. The villagers begin to play music and dance but Jaguar Paw's mind is distracted until Seven brings him back.
The following morning, Jaguar Paw wakes early from a dream and notices fire torches quickly approaching the village. Warriors appear, igniting huts and apprehending the villagers. Jaguar Paw takes his wife and son and puts them in a deep cistern to hide. He ties a rope to a nearby rock so that they can climb out again before running back to the village to help, killing a raider along the way. However, the village is soon overrun. Blunted is held down while Sky Flower is forced into a hut where she is presumably raped and killed. Jaguar Paw attempts to free his father but is knocked down by a raider. Middle Eye (Gerardo Taracena
), a raider nearly killed by Jaguar Paw, nicknames him 'Almost'. Flint Sky tells his son not to be afraid as Middle Eye props him up and slits his throat. All the surviving captives are tied up and led away, attached to each other on long poles while the children of the village are left with none but the dead for company. As the Holcane hunting party leads the captives into the forest, one of them, Snake Ink (Rodolfo Palacios
), notices Jaguar Paw looking towards the cistern as they pass. Snake Ink investigates but does not notice Seven and Turtles Run. He is, however, suspicious of the rope dangling into the hole and cuts it.
The fierce-looking leader of the Holcanes, Zero Wolf (Raoul Max Trujillo
), reunites with his son Cut Rock (Ricardo Diaz Mendoza
) who has suffered a bruising blow to the head, swelling his right eye shut. Zero Wolf cuts lines into his brow to release the pressure of blood, allowing his son to see again. The party meets up with a second raiding group which has caught the band of refugees seen the day before. Jaguar Paw recognizes the fisherman as the two groups are led further into the forest, followed by the children of the two clans. As they cross a raging river, the children are halted by the water. The eldest girl cries out that the children are hers now and she will take care of them. That night as they camp, Zero Wolf gives his son a large dagger which he says has killed many men. It is a symbol of Cut Rock's manhood, proven by the successful raid. Blunted laments and promises to take as many captors with him to Hell if he does not find his Sky Flower there.
The next day, while treading a narrow path on a cliff, Cocoa Leaf, severely injured in the village raid, looses his footing and dangles over the edge. Jaguar Paw and the others manage to pull him back onto the path while Middle Eye watches with interest and goads them to regain their footing. He then cuts Cocoa Leaf free of his binds and shoves him over the cliffside. Zero Wolf berates him for losing one of their captives though Middle Eye asserts he was only dead weight. Still, Middle Eye dares not argue further and assures not to repeat his actions before walking beside Jaguar Paw, taunting him and again calling him 'Almost'.
As they near civilization, the party crosses through a deforested area and failed maize crops where villagers lay dead, decimated by a plague. A small girl, sick and with sores on her face and hands, approaches the party but, when Snake Ink forcefully pushes her away, suddenly looks towards Jaguar Paw with a blank expression. She then looks at Snake Ink and prophesies their doom, warning of a man who brings blackness of night and a jaguar, is reborn of mud and earth, and who will bring those that will cancel out the sky and 'scratch you out'. She says that this man is among them now. The party moves on as she continues to call to them.
They enter a city where workers toil in limestone quarries, covered white by the excess and spreading quick lime over buildings. A worker coughs blood and an old man approaches the captives, drooling and begging for help. He is kicked away by a Holcane and told to die with dignity. The women captives are separated from the men and are sold as slaves. Blunted watches as his mother-in-law is auctioned but rejected due to her age. She is freed to wander and she follows Blunted as far as she can go, touching his arm assuredly before closing her eyes against a pillar, helpless.
The men are led through a tunnel where they see pictures on the walls depicting human sacrifices. Women paint their bodies blue as they are led to the top of a step pyramid. The heads of victims are tossed down the steps and collected in baskets at the bottom. Jaguar watches as the first captive (José Suárez
) is sacrificed, his heart ripped out and his head severed. The same fate befalls Curl Nose before Jaguar Paw is brought to the sacrificial pedestal. Seemingly accepting his fate, he waits until the high priest (Fernando Hernandez
) stops due to a solar eclipse. The priest announces to the clamoring crowd that their god is pleased and begs for the sun to come back. However, the priest and the Mayan leaders are well aware that the eclipse will eventually pass; they use the celestial events to wield power over the public and their enemies. He then instructs Zero Wolf to get rid of the other captives.
Jaguar Paw and the others are taken to an old ball court where they are instructed to run the length in pairs towards the forest at the end with a cynical promise of freedom should they make it. Cut Rock runs ahead to the end of the court as a 'finisher' and it becomes clear that the captives are to be used as target practice. Blunted and Smoke Frog are the first to run, but Blunted is speared in the lower back and Smoke Frog is hit with a large stone before being finished by Cut Rock. Next, Jaguar Paw and the fisherman are told to flee. Jaguar Paw's necklace is ripped off by Middle Eye and thrown into the dirt; a dark omen, before he runs. Though they evade most of the projectiles, the fisherman is shot through the head by Snake Ink's arrow and Jaguar Paw is impaled through his side, falling near Blunted. Before Cut Rock can finish him, Blunted lunges and grabs Cut Rock by the leg, buying Jaguar Paw some time. Cut Rock kills Blunted with a single blow to the head but Jaguar Paw breaks off the arrow head in his own body and stabs Cut Rock in the neck. Cut Rock stumbles as Jaguar Paw stands, removes the arrow shaft from his side, and runs into the forest.
Zero Wolf runs to his son and coaxes him into eternal sleep. As his son dies in his arms, Zero Wolf takes back his dagger and puts his son's necklace into his belt before running after Jaguar Paw, bent on revenge. The other holcanes follow him. Jaguar Paw runs through a corn crop and falls into a mass open grave filled with the remains of thousands of sacrificial victims. He runs across the decaying bodies into the jungle, where he climbs a tree and hides, blood still dripping from his wound. The holcanes run past beneath him. When they are gone, he turns to see a black jaguar cub growling at him. He hears a louder roar behind him and turns to see the threatening mother jaguar. Meanwhile, the holcanes stop, realizing they have lost Jaguar Paw's trail. One of them notices blood on Middle Eye's shoulder and they backtrack, keeping their eyes to the trees. They soon see Jaguar Paw running through the forest and Speaking Wind (Marco Antonio Argueta
) pursues him. As their paths merge in a clearing, Speaking Wind is attacked by the jaguar that was chasing Jaguar Paw. He is viciously mauled to death before the others arrive and kill the jaguar.
Drunkards Four (Bernardo Ruiz
) dislikes the bad omen associated with killing the jaguar while Snake Ink remembers the strange child's prophecy and remind him it was foretold. Zero Wolf hushes them all, eager to find and kill Jaguar Paw. The chase lasts through the night and into morning. At one point, Drunkards Four approaches a tree where blue paint which Jaguar Paw rubbed onto the tree, but he is bitten in the neck by an asp. Hanging Moss (Ariel Galvan
) advises him to blood let for a quicker death. As the holcanes eventually catch up to Jaguar Paw, he is cornered and forced to leap over the edge of a high waterfall. He survives and stands on the riverbank, calling out to the holcanes that this is his forest and his descendants will continue to hunt in it. Impatient, Zero Wolf stabs Snake Ink when he suggests climbing down rather than jumping. Buzzard Hook (Ammel Rodrigo Mendoza
) is the first to jump, but dies when he hits his head on a submerged rock. The others are luckier and continue their pursuit.
As he flees, Jaguar Paw lands in a muddy sinkhole, but manages to climb out. After he does so, he pauses and decides that he is not afraid and will no longer run. As the holcanes approach, Jaguar Paw, covered in black mud, confronts them and tosses a live wasps' hive at them, instigating the wasps to attack. Jaguar Paw runs towards a stream where he finds a poison arrow frog and collects its venom on a few large thorns. He runs in a circle and hides in the reeds, waiting for the holcanes as thunder rolls overhead.
Meanwhile, Seven attempts to escape the cistern by tossing a stalactite to the surface with the rope attached to it. She manages to climb halfway, but the rock dislodges, causing her to fall. Though she is barely hurt, her water breaks from the trauma.
As the holcanes pass Jaguar Paw's hiding place, he takes a large leaf and rolls it into a blowgun. He fires his darts at Hanging Moss, already weakened by the wasp stings. As Hanging Moss falls to the ground, his cries attract Middle Eye, who runs back. Middle Eye comes face to face with Jaguar Paw and they run at each other, each eying the bludgeon that Hanging Moss dropped. Middle Eye swings his own as they approach each other and Jaguar Paw barely manages to duck, suffering a mild blow to the head. As he slides under Middle Eye's attack, Jaguar Paw picks up Hanging Moss' bludgeon and rises to strike Middle Eye in the temple. Middle Eye calls him Almost one last time as Jaguar Paw kills him with a blow under the chin. It suddenly begins to rain and Jaguar Paw races to the cistern, knowing that it will soon fill with water. Zero Wolf and the remaining holcanes, Monkey Jaw (Carlos Ramos
) and Ten Peccary (Richard Can
), see Middle Eye's body and Jaguar Paw racing into the forest. Enraged, Zero Wolf outruns the other two in his pursuit. Jaguar Paw gets to the cistern to find it filling with water and Seven in labor, screaming for him to hurry. An arrow narrowly misses Jaguar Paw and he runs into the jungle as Zero Wolf closes in. Monkey Jaw and Ten Peccary pause by the cistern to see Seven and Turtles Run at the bottom before resuming the chase.
Jaguar Paw stops at a specific spot in the forest that he recognizes and turns to face Zero Wolf who shoots an arrow into his shoulder. Though wounded, Jaguar Paw stands, waits, and watches as Zero Wolf charges at him with his dagger drawn. Zero Wolf fails to notice a trip wire and sets off the tapir trap, becoming impaled on its sharp spikes. He dies as Monkey Jaw and Ten Peccary arrive. They chase Jaguar Paw to the beach where he collapses from exhaustion. When they catch up with him, they stop, staring at the sea where a small fleet of Spanish ships is anchored. Soldiers and missionaries are rowing to shore in small boats. Mesmerized, Monkey Jaw and Ten Peccary approach the shoreline while Jaguar Paw races back to the cistern. He finds that Seven has just given birth and pulls his family out of the cistern.
Later, when the rain stops, Jaguar Paw carries his newborn son, followed by Seven and Turtles Run. They look back towards the Spanish ships and Seven asks if they should go to them. Jaguar Paw says that they should, instead, go to the forest and seek a new beginning.