Genetic engineering on trees was conducted at a research facility on the Moon to produce trees capable of growing in harsh, arid conditions. The trees gain consciousness, obliterating Earth's civilizations and destroying the Moon. Three hundred years later, Japan is a dystopia covered by the Forest, a huge expanse of sapient trees, and ruled by the tree-like Druids, which inhabit the planet and control the water supply of both trees and humans. Agito, a young boy, and his father Agashi, as well as his friends Cain and Minka, live in Neutral City, a city carved out of the ruined skyscrapers which acts as both a buffer and a bridge between the Forest and the militaristic nation of Ragna. While the people of Neutral City co-exist peacefully with the trees of the forest, the nation of Ragna aims to destroy the Forest to restore the Earth.
One day, Agito and Cain race each other to see who can get to the water hole at the bottom of the city first. By disturbing the sanctity of the water hole and angering the Druids, the two boys are separated. After stumbling upon a large machine with cryogenic pods, Agito accidentally revives Toola, a young girl who has been asleep for the past 300 years, and brings her to Neutral City. The Forest is angered by Toola's awakening, since she carries a Rabanâa portable personal electronic device, worn as a necklace, that can be used for communication and a variety of other tasks. The Forest fears that she will fall into the hands of Shunack, a soldier of Ragna and also a person from the past who was awakened from sleep, and that he will use her Raban to locate E.S.T.O.C., an "environmental defragmentation system" with the ability to wipe out the Forest and restore human control over the world.
Shunack finds out about Toola and arrives into Neutral City with his army to persuade her to join him. The Forest sends a giant creature to stop the meeting, but Shunack destroys it and reveals that he has been "enhanced"âhe allowed himself to be genetically altered by the Forest to become stronger by using the power of the trees. Convinced that finding E.S.T.O.C. is the only way to restore the Earth back to the world which she once knew, Toola joins Shunack in his quest despite Agito's plea not to go. Agito consults his father Agashi, the founder of Neutral City who, as a result of being enhanced and having overused his powers, has turned almost completely into a tree. With few days left before becoming a tree completely, Agashi encourages his son to save the Forest from Shunack's plan, since destroying the trees would mean the destruction of mankind. Agito journeys to the Forest and allows himself to be enhanced, his hair turning silver as a result.
Agito follows Shunack and Toola to E.S.T.O.C., a giant volcano converted into a mechanized weapon. E.S.T.O.C. was created by Toola's father Dr. Sakul, the doctor who had begun the genetic research on the trees, as a safeguard against the new species. Betraying the Ragna army and focusing his attention on E.S.T.O.C., Shunack reveals that he worked on the original genetic alteration experiments on the trees. However, his impatience to speed up the alteration process resulted in the catastrophic invasion of the mutant trees. Shunack intends to activate E.S.T.O.C. to return the world to the way it used to be and so right the damage he had caused and the guilt that has plagued him ever since. However this will destroy the world that has formed in the old one's place. Shunack plans on activating E.S.T.O.C. near Neutral City, thus obliterating it. When Toola realised this, she fights Shunack to prevent him from activating E.S.T.O.C. As the Ragna army commences their assault on E.S.T.O.C., Agito faces Shunack. Agito transforms into a tree in a desperate attempt to save Toola, trapping Shunack within it. Toola shuts down E.S.T.O.C. and the weapon's self-destruct sequence is initiated. Having developed strong feelings for Agito, Toola is unable to leave without him.
Meanwhile, Agito's consciousness remains intact on another plane, and there the Forest reveals to him the truth about the relationship between itself and the humans. Agito learns that the genetic admixture that gives humans extraordinary strength and eventually turns them into trees is really a two-way exchange; it also changes the Forest, causing trees to give birth to new humans in giant fruits. Having become one with the Forest, Shunack is now at peace and no longer intends to fight Agito. Realizing that Agito can teach humanity that there is no need for either hostility or separation between themselves and the trees, the Forest returns Agito to his true form, allowing him and Toola to flee before E.S.T.O.C. is destroyed. With the humans and the Forest saved, Agito brings peace between humans and the trees. Toola finally lets go of her past by throwing her Raban off a ledge down into the depths of the Forest, learning to live in harmony with the trees at last.
Who searches their souls?