Since his parents' deaths, Yagi Takeru has been living at the Touma family's home. Touma Rokunosuke, the house's leader, reared him. Yamato Takeshi, his closest buddy-cum-rival from the kendo club, the Shiratori sisters, Kotono and Asuka, and his childhood friend, Oosu Seri are all around him. Life had been idyllic until one day, when an earthquake struck the school, and everything changed. Takeru awakens to discover that the school has been abandoned for generations and has been reduced to ruins. He also notices that all of the professors and pupils have vanished. He joins up with Seri and Asuka, and they flee the ruins, only to discover that the town they used to live in is no longer there.