Agito, a teenager in Neutral City—a settlement carved from a decaying metropolis serving as a buffer between the sentient Forest and militaristic Ragna—grapples with his father Agashi’s legacy. Once a co-founder of the city, Agashi sacrificed his humanity through Forest-bestowed genetic enhancements, gaining power in exchange for becoming a tree. Agito navigates friendships with Cain and Minka while balancing the city’s fragile harmony with the Forest, which enforces strict dominion over water.

During a reckless race to a forbidden spring, Agito awakens Toola, a cryogenically preserved girl from the pre-collapse era. Her revival draws the Forest’s wrath due to her Raban, a relic tied to an ancient weapon system. Protecting her, Agito clashes with Shunack, a survivor from Toola’s time determined to annihilate the Forest and reclaim human supremacy. Guided by his near-arboreal father, Agito learns the Forest’s survival is intertwined with humanity’s fate.

Choosing his father’s path, Agito undergoes genetic enhancement, gaining superhuman abilities as silver streaks his hair—a harbinger of his accelerating transformation. At E.S.T.O.C., a volcanic superweapon built by Toola’s father, Agito confronts Shunack, whose guilt over triggering the apocalypse fuels his crusade. In their final clash, Agito fully transforms into a tree, absorbing Shunack and halting the weapon. Merging with the Forest’s hive mind, he discovers their symbiosis: humans and trees exchange genes, enabling the Forest to birth new humans, weaving a shared future.

The Forest resurrects Agito’s human form, cementing his role as a bridge between worlds. His sacrifice inspires Toola to abandon her Raban, embracing the reborn Earth. Agito’s legacy endures as a testament to coexistence—a equilibrium where neither humanity’s resilience nor the Forest’s sentience prevails, but both evolve together.