Three decades ago, more than a hundred million people fell victim to an unprecedented disaster that came to be known as a "spatial quake." Ever since then, humanity has built countermeasures to mitigate the damage from future catastrophes such as instantaneous evacuation methods and immediate rebuilding of any architectural damage. At present, 16-year-old Shidou Itsuka lives alone with his sister, Kotori. One day, he gets caught in a spatial quake despite preemptive warnings. Miraculously surviving the blast, he meets a mysterious girl in its wake, who he soon comes to know as a "Spirit"—supernatural beings who are the cause behind these spatial quakes. Coincidentally, he learns of the "Anti-Spirit Team," a specialized military unit tasked with destroying these Spirits with brute force.