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A Certain Magical Index is set in a world where supernatural abilities are a reality. While some individuals known as Espers (???? Chonoryokusha?) possess special powers gained since birth, other individuals denominated Magicians (??? Majutsushi?) gain their powers upon mastering the power of symbolism, be it from obtaining knowledge from special books known as Grimoires (??? Madosho?) or by using special magic artifacts. While several Magician cults align themselves with ancient religions, Esper powers are usually developed by experimentation and training, thus they are usually aligned with scientific institutions. This leads to a power struggle between magic and science factions for control of the world.

The story is set in Academy City (???? Gakuen Toshi?), a technologically advanced city located in western Tokyo, known for its educational and research institutions. Toma Kamijo is a student in Academy City whose right hand, the Imagine Breaker, has the ability to negate any supernatural powers, but also negates his own luck, much to his chagrin who meets a young girl named Index who is a nun from Necessarius, a secret magic branch of the Church of England, and her mind has been implanted with the Index Librorum Prohibitorum-103,000 forbidden magical books the Church has removed from circulation. His encounter with her leads him to meet others from the secret worlds of science and magic and an adventure with his friends where both collide. Toma's unusual power places him at the center of conflicts relating magicians and science-based espers in Academy City. As Toma tries to help and protect his friends, he learns the people heknows are not as they appear and begins to attract the attention of magicians and espers alike as they try to unravel the secrets behind Academy City, Index and his own special power.

The side-story A Certain Scientific Railgun focuses on Mikoto Misaka, an electromaster who is the third most powerful of the seven Level 5 espers in Academy City. Set before and during the events of the novels, the manga tells the adventures of Mikoto and her friends during that time period from their point of view. Another side-story, A Certain Scientific Accelerator, focuses on Accelerator, a telekinetic known as the most powerful esper in Academy City, who like Mikoto is a prominent character in the main story.