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.

During the crisis at the nuclear power plant, Juna (who is still learning to deal with her powers) receives the Holy Bow Gandiva.. but when she panics, she somehow calls us Ashura, the many-armed 'Protector of Time' who fights the Raaja for her. Meanwhile, Chris tells Juna that her job is NOT to destroy the Raaja, but to purify them. Chris takes over the fight, but Juna wants to prove that she can help him without destroying everything.

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.

S.E.E.D. rushes Juna to New York because her powerful TI counterpart there has fallen. There, she witnesses one path that a society can take. This society is built upon the ever-increasing garbage heap caused by mass consumption. Because of this, many people do not truly enjoy their lives. Can humanity break this cycle?

The cataclysm begins. Huge droves of Raaja invade Japan, plunging the human population into chaos. However, driven by the will to survive, humanity perseveres in the vortex of the brewing storm. Tokio refuses to believe that hope is lost and resolves to save Sayuri and the others. Meanwhile, S.E.E.D. is virtually holding Juna captive in its American branch. Juna anguishes over her inability to rescue Tokio, her mom, or her sister. Can she release herself and save those she holds dearest?