 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 its parent company Asgard Electronics, and is recruited to make use of his mysterious ability to seal the Spirits' powers thus stopping them from being a threat to mankind.