One year has passed since the events at mount Minakami, Sho and Agito have disappeared, and Cronos has taken complete control over the world, affecting life in many aspects.

Tetsuro, Mizuki, Shizu and Yohei hide in a small apartment, waiting for the heroes' return. Aptom spies on them, and even keeps their existence away from Cronos when authorities may discover them.

At Cronos, dr. Balcus is carrying on a mysterious experiment on a new creature, and receives the visit of Shin, one of the Zoalord Divinities, who asks him to intervene on the Dead Sea, where a strange phenomenon is happening.