Origin: Spirits of the past

Origin: Spirits of the Past is the story of Agito, a young boy living in a dystopian Japan set 300 years in the future. This apocalypse was brought about by extensive genetic engineering on trees, conducted at a research facility on Earth's moon, in order to produce trees capable of growing in harsh, arid conditions. The trees became conscious and spread to Earth in a fiery holocaust, wiping out most of modern civilization and fragmenting the moon. Agito's world is covered mostly by the Forest, a huge expanse of living trees, ruled by the tree-like Zruids, which now inhabit the earth and control the water supply of both trees and humans. Agito and his father Agashi, as well as his friends Cain and Minka, live in Neutral City, a city carved out of the ruined skyscrapers of an old metropolis. Neutral City 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 in order to return the world to the way it was before the mutant trees invaded.

The movie starts with Agito and his friend Cain racing 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 Zruids, the two boys are separated, and Agito stumbles upon a large machine with cryogenic pods containing mostly dead bodies. Inside the only active pod he finds Toola, a young girl who has been asleep for the past 300 years. He revives her and then brings her back with him to Neutral City. The Forest is angered by Toola's awakening, since she carries a Raban — a 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. (Environmental Defragmentation System), a powerful weapon with the ability to wipe out the Forest and restore human control over the world.

Shunack eventually finds out about Toola and marches into Neutral City with his army to persuade her to join him. The Forest sends a giant creature to stop the meeting, which Shunack single-handedly destroys, revealing that he has been "enhanced" — he allowed himself to be genetically altered by the Forest in order 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. Agashi, with few days left before becoming a tree completely, encourages Agito to save the Forest from Shunack's plan, since destroying the trees would mean the destruction of mankind as well. 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., which turns out to be a huge volcano converted into a mechanized weapon. E.S.T.O.C., as it turns out, was created by Toola's father, the doctor who had begun the genetic research on the trees, as a safeguard against the new species. Shunack betrays the Ragna army and commandeers E.S.T.O.C., revealing his true intentions to use the weapon to clear his guilt: it so happens that Shunack worked on the original genetic alteration experiments on the trees, but, becoming impatient, had tried to speed up the alteration process, leading to the catastrophic invasion of the mutant trees. When Toola learns that Shunack intends to activate E.S.T.O.C. on Neutral City, destroying it completely in the process, she has a change of heart, tries to stop Shunack from activating E.S.T.O.C., but is quickly overwhelmed. Agito finds them and has a showdown with Shunack. To save Toola, he lets his enhancement take him over, and he transforms into a tree, essentially killing himself and Shunack in the process. Toola deactivates E.S.T.O.C. and the weapon begins to self-destruct; however, Toola refuses to leave without Agito, having developed strong feelings for him.

Although Agito's body has been absorbed by the tree, his consciousness is 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 (This may possibly be a reference to the "Peach Boy" legend). Shunack, having become one with the Forest, finds peace with himself and no longer intends to fight Agito. The Forest, seeing that Agito can teach humanity that there is no need for either hostility or separation between themselves and the trees, grants him his human form back, allowing him and Toola to escape before E.S.T.O.C. erupts into flames. Having saved both the humans and the Forest, Agito brings peace between all 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 and learning to live in harmony with the trees at last.