The series begins with a strange phenomenon called "spatial quake" devastating the center of Eurasia, resulting at least 150 million casualties. For the next 30 years, smaller spatial quakes plague the word on an irregular basis. In the present, shido itsuka, a seemingly ordinary high schooler come across a mysterious girl at the ground zero of spatial quake. He learns from his adopted sister kotori that the girl is one of the "Spirits" from different dimension whom are the real cause of the spatial quakes that occure when they manifest themselves in the real world. Shido's intelligent classmates, Origami tobiichi, is a sergeant of the AST (Anti-Spirit Team) special unit designed to suppress the threat posed by spirits to exact revenge of her parents deaths. He also learns that kotori is the commander of the airship <Fraxinus>, crewed by the organization <Ratatoskr>, and is recruited to make use of his mysterious ability to seal the spirits powers thus stopping them from being a threat