Amami Kouji lost his parents in an accident when he was a child. After that he was adopted by his father's friend Kusanagi Keisuke, the chief priest of the Shinto shrine of Misaka City. Since then he has lived with Keisuke and his daughters, Makoto and Minato.
In the accident he didn't lose only his parents, but his left eye as well. Now he is learning the art of swordsmanship and he's too good for someone with only an eye: even though his left eye can't see anything, it allows him to “see” impending dangers and other people's killing intent as “lines”. He calls them “death lines”.

One day he's having lunch on the rooftop of his school with Makoto, Minato and his friend Kaiji, when he notices a girl, Hirasaka Suzuka, getting bullied by three girls. After rescuing her they make friend.
Two days later he meets a girl, Haruka Lichtenbein, who recently moved from England to Misaka and got lost on her way home, and decides to help her.

As the time passes by, strange events happen in his city. Strange monsters appear and attack girls on night. And a strange blond-haired guy seems to have something to do with all these events...