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.

The SEED helicopter drops Juna off in the middle of the mountains to get her to commune with nature and learn to survive in the wild. Chris explains to an angry Tokio that the Earth is reaching a point where it can't put people's lives before its own needs. Tokio visits Juna's mother, who thinks that he's become a liar just like everyone else. As Arjuna slowly learns to resonate with the world around her, Tokio discovers a Raaja lurking within a landfill on the mountain.

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.

Juna and Tokio return to the city and meet up with their classmate Saiyuri, while Teresa informs her SEED commander of a virus that's spreading over western Japan from genetically engineered agriculture. At a fast food restaurant, Juna learns one the perils of her new power, but all this is overshadowed when Tokio contracts the virus. Juna is sent into Tokio to save his life from the Raaja that lurks within both of them.

Recovered from the virus, Juna and Tokio are ready to adjust to normal life again when Juna's father shows up, leading to a strained conversation between father and daughter. When school starts up again, Raaja appear during Juna's math class, and Chris shows up once again in the middle of the battle. When Juna and Tokio follow the math teacher home, Juna learns about his life and passion for teaching, but Tokio, as does the rest of society, sees his discussion as worthless and confusing.

Confused by Juna's transformation, Tokio begins pulling away from her and spending more time with another girl named Sayuri. To make matters even more surreal, Juna can now see Tokio's uneasy thoughts take physical form! Meanwhile, Chris's body wilts and falls ill after confronting the Raaja all over the world. Cindy, his companion, summons Juna to S.E.E.D's underground sanctum to rescue him. When Juna reaches Chris, a mysterious power envelopes them all ...

Will down pouring rain fill a person's heart with sorrow? The stress of the ongoing crisis is wearing down the bond between Juna and Tokio. Although she may wield the holy Gandiva weapon, Juna is still a teenage girl at heart. Since Juna became the chosen one, she and Tokio have been acting more awkward around each other. Despite their mutual feelings, the couple seems to only disagree. Sayuri, Juna's rival, seizes the opportunity to make her move. Only the rain embraces a distraught heart...

Juna rushes towards Japan and Tokio as the final struggle begins. Swarms of Raaja bury the streets of the cities. From Juna's holy bow Gandiva, countless arrows rain down upon the amassed creatures. As Juna loses herself in her anger, the final enemy appears before her...

Juna's heart is in turmoil when she sees Tokio and Sayuri together. However, Cindy can see through Tokio's confused emotions with her telepathic gifts, and tells Juna that she and Tokio are not through yet. First, Cindy tries to help Juna understand her own feelings. Cindy guides Juna back in time to her own mother's womb, where her thoughts first formed ...

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.

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?