Yagi Takeru has been living in the Touma family's house since his parents are gone. He was raised by Touma Rokunosuke, the head of the house. He is surrounded by many people such as Yamato Takeshi, his best friend-cum-rival from the kendo club, the Shiratori sisters, Kotono and Asuka, and his childhood friend, Oosu Seri. Life has been blissful until one day, an earthquake strikes the school and everything changes. Takeru awakens to find that the school looks as if it has been abandoned for centuries and reduced to ruins. He also realizes that all the teachers and students have disappeared as well.