Thirty years ago, the Eurasian continent was ravaged by a colossal "spatial quake"—a phenomena involving unexplained space vibrations—that killed over 150 million people. Since then, these quakes have been affecting the planet on an irregular basis, albeit on a smaller scale. Shidou Itsuka is a fairly ordinary high school student who lives with his younger sister, Kotori. When an impending spatial quake threatens the safety of Tengu City, he hurries to help her, only to be ensnared in the ensuing eruption. He discovers a mystery female at its source, who is revealed to be a "Spirit," an extraterrestrial being whose arrival causes a space quake. Soon later, he becomes involved in a fight between the girl and the Anti-Spirit Team, a brutal strike.