Sacred stones are implanted in the bodies of two boys. Decades later, the world is divided. There are those who want to eliminate the "kaijin" and those who want to coexist with them. In the midst of this, there is a man, Kotaro Minami who's somewhat a recluse. A young activist, Aoi Izumi wants to change the divided world. When Aoi and Kotaro meet, the time which had stopped begins to move again.

After the attack, Aoi and Kotaro find themselves in a strange relationship. Meanwhile, Bilgenia, who had obtained video evidence from Kawamoto, the wanted man doesn't tell Dounami about it. In the midst of all this, the protest that Aoi participates in develops into violent clashes and chaos. Then suddenly Nobuhiko Akizuki appears, insisting on the rights of the kaijins and rousing them to action.