Modern magic aims to fuse science and magic. One of such modern magi, Amami Shuu, is told that his classmate, Natsuki Kaori, saw her doppelganger. Shuu begins looking into the case as rumors of people disappearing after seeing their doppelganger make the rounds. One day, he finds another classmate, Kouno Mio, fighting a doll-like, blue haired girl. A few days later, this girl shows up as a transfer student in their class, calling herself Momono Shiori. With their objectives aligned, they begin a battle against the unknown.

[Translated from the game box synopsis]

Utsuro naru Kyoukai is a whole new story with new characters and concepts that takes place parallel to the events of 11eyes -Tsumi to Batsu to Aganai no Shoujo-.