Despite 80% of its 2.3 million population being students, Academy City is far more advanced than any other nation worldwide. Its residents awaken something akin to a supernatural ability inside them, which is then ranked from Level 0 to 5. Along the lines lies Touma Kamijou, a powerless Level 0 esper. While his abilities are recognized as useless, he possesses a mysterious phenomenon known as "Imagine Breaker," which allows his right hand to nullify any supernatural powers upon coming in contact with them. Despite that, he claims to have rotten luck due to the misfortunes that frequently happen to him.

One day, a girl calling herself Index Librorum Prohibitorum mysteriously lands on Touma's balcony and explains to him that she is being hunted down by magicians. This leads the powerless boy to discover a whole new world—one where magic exists. With Touma facing the problems that arise from both the scientific and magical sides of the world, how will he resolve them?