Juna, a high school student who does traditional Japanese archery, is riding along the seaside on her friend Tokio's motorcycle when they get into a mysterious accident and she dies. As her spirit floats away, a boy stops her and tells her he will grant her a second life if she will fight to defend the Earth from the strange 'worms' called Raaja. We also meet the mysterious organization SEED, who are on scene at a disaster involving the Raaja at a nuclear power plant.

As Chris encourages Juna to learn to use her power on her own, Juna and Tokio find their way out of the mountains to the home of an old man who lives a completely organic/Earth-friendly lifestyle. In exchange for food and shelter, they help with gardening. Juna seeks to understand the strange shadows and pictures she can now see while looking at plants and food while Tokio bonds with the older man. When Juna sees a Raaja attacking the rice paddy, Tokio must force her to use her eyes as well as her powers.

Juna travels alone to a laboratory endangered by a biohazard disaster. However, the man in charge is none other than Tokio's father. He dismisses Juna's concerns, seeing them only as the vague visions of one little girl. Tokio arrives, but the friction between him and his father only heats the debate even more.