The series begins with a strange phenomenon called a "spatial quake" devastating the center of Eurasia, resulting in at least 150 million casualties. For the next 30 years, smaller spatial quakes plague the world on an irregular basis. In the present, Shido Itsuka, a seemingly ordinary high school student comes across a mysterious girl at the ground zero of a spatial quake. He learns from his adoptive sister Kotori that the girl is one of the "Spirits" from different dimensions who are the real cause of the spatial quakes that occur when they manifest themselves in the real world.
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 to mankind. However, there is a catch: to seal a Spirit's power, he must make her fall in love with him and make her kiss him. Shido's intelligent classmate, Origami Tobiichi, is a sergeant of the AST (Anti-Spirit Team), a special unit designed to suppress the threat posed by Spirits.
As Shido successfully keeps sealing more and more Spirits, he gains allies to help him with his dates with other Spirits. Shido also increases the competition among them for his attention and affection, much to his chagrin.