Thirty years ago, the Eurasian continent was devastated by a phenomenon of space vibrations of unknown origin. More than 150 million people died and the quakes have been mild ever since. One day, when another spatial earthquake threatens his city, high school student Shidou Itsuka rushes to save his sister Kotori. A mysterious girl, a Spirit, turns out to be the source of the alien quake. Shidou soon becomes involved in a skirmish between the girl and a group that hunts Spirits. However, there is also another party that wants to save the girls, led by Shidou's sister.