In the land of Mezo, the Tzalekuhl Empire sets out to conquer the surrounding territories, determined to make all other tribes kneel before their god, Kuhl, or be sacrificed in his honor. They believe it is the only way to ensure their safety during the upcoming solar eclipse, after the last one caused a volcanic eruption that destroyed their previous home: an event known as "The Rupture."

During the first Tzalekuhl invasion, Kyma witnessed the death of her father, chief of the Huax'kin, at the hands of the supernaturally strong Phegor. Kyma's life was spared by a kind soldier named Roden. Eventually, Kyma escaped and lead the surviving members of her tribe deep into the forest where she reunites with her estranged mother, Mz'ira, chief of the Kan'kin. Their only chance of standing up against the Tzalekuhl is to unite their forces.

But the Tzalekuhl know exactly where they're hiding thanks to their mystical power of Ne'nezi. He was once of member of the ancient order known as the Zen'talli, but now serves Emperor Vuh. They send their troops into the jungle towards Cobán Rock to wipe out the tribes once and for all.

Meanwhile, Itza'be, the last remaining member of the Zen'talli, jouneys to the World Tree to consult the Great Mother. He learns that his failure to join his fellow Zen'talli during the previous solar eclipse likely caused "The Rupture." Each member of the Zen'talli carries with them 1/3 of the Celestial Seed, diving its power among them. If he doesn't reunite the Seed before the next eclipse, the devastation will be even more severe this time.

Itza'be sets off toward the now unguarded Tzalekuhl palace, bringing with him his young disciple, Zea. They seek Ne'nezi so they can use his part of the Celestial Seed in order to find the missing third piece, lost at the city of Meztalpotek during "The Rupture."

Back at Cobán Rock, the Tzalekuhl forces are overwhelming the tribes until the Hero Twins, Uhna and Balaque, show up with the giant tree creatures known as the Arbath'a. They want to put an end to the battle, but it's tough to play peacekeeper when you show up after the bloodshed has begun. Their objective if further complicated when they realize their old friend, Roden, is leading the Tzalekuhl. During their hesitation, Kyma tries again to avenger her father, but Phegor is too strong. Mz'ira jumps in to save her daughter and sacrifices herself in order to buy time for the tribes to escape.

Phegor takes over command after discovering that Roden's allegiance to the empire is compromised. He orders the pursuit of the tribes. No one must be allowed to escape. But the hero twins have other plans and hold off the Tzalekuhl until the tribes have all crossed the ravine, cutting the bridge down behind them. Phegor and the Tzalekuhl may have won the battle, but the tribes remain free.

After burying her mother, Kyma asks the hero twins to join her in a journey back to the Tzalkuhl. Their mission is two-fold: rescue their friend Roden and discover what has happened Itza'be and Zea. The eclipse is fast approaching, and if the Celestial Seed is not reunited in time, it will be the doom of all on them.