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.

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?