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.

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 ...