The story starts in a big city where 2.3 million people reside; it is so big that it occupies most of the western region of Tokyo. As 80% of the citizens are students, it is called an academic city. They have special curriculums that develop supernatural abilities, and the students are sorted into different levels, from level 0 to level 5, depending on their supernatural power.The protagonist, Komijo Toma, is also a student but he is ranked level 0, and is close to dropping out of the school. In his right hand, there resides a special power, â€œImagine Breakerâ€, that nullifies any other supernatural powers; the power even nullifies the saving grace of God.One day, during the summer break, a Sister in white falls into his room from the air. The nun says that she is running away from the magical world, and names herself Index, or the Index of Prohibited Books. Although he lives in a city in which supernatural powers are taken for granted, he cannot help but suspect the fantastic story told by this girl who must have given him a false name. At that very moment, two wizards appear. Their target is the girl in white, Index.