Index is still a fugitive, and many powerful magical organizations and individuals want to take her to use the books in her memory, eliminating her in the process. War between those organizations is also starting to emerge. Index can only rely on her friend Touma, who has always protected her, along with Misaka and other friends from the Academy.

The Daihasei Festival is under way and the prestigious Tokiwadai Middle School, where the Ace of Tokiwadai, Mikoto Misaka reside, is one of the schools participating in this annual sports fest. However, not all are fun and games as people behind the shadows start to plot a new threat that will endanger Mikoto and the whole Academy City. After the Daihasei Festival, Mikoto and her friends find themselves being involved in multiple incidents surrounding special cards that supposedly record people's dreams.

Something sinister is going on in Academy City. The shadows are filled with whispers of an organization cloning super-powered students known as espers. High-ranking master of electricity, Mikoto Misaka, laughs off these stories until she comes face to face with a copy of herself. After learning that these clones — her sisters — are being systematically murdered in a series of experiments designed to turn a sadistic killer into the strongest esper in history, Misaka vows to save her copies and destroy the organization responsible for the project. As Misaka prepares to face off against the organization’s power-hungry esper, she discovers that she wasn’t the only victim of the scientific forces conspiring within the city — and that’s something Misaka and the girls of Judgement simply won’t stand for.

Academy City is a highly developed place in terms of technology. It is said to be 20 to 30 years ahead of the rest of the world, and 80% of its 2.3 million residents are students. The focus of studies here is directed towards esper powers. Misaka Mikoto, one of the top level espers in town, shares a room with Kuroko Shirai, another high level esper who is a member of Judgement, a law enforcing agency composed of students. Both attend Tokiwadai, a private school reserved for the high-leveled and the rich. Kuroko's partner at Judgement, Kazari Uiharu, is a low level esper who studies at Sakugawa middle school. Her best friend and classmate there is Ruiko Saten, a level zero, one who has no esper powers. Together, the four encounter several adventures in the exciting scientific town.

Set in a city of scientifically advanced superhuman students, but in a world where magic is also real. Touma Kamijou’s right hand, the Imagine Breaker, will negate all magic, psychic, or divine powers, but not his own bad luck. One day he finds a young girl hanging on his balcony railing. She turns out to be a nun from the Church of England, and her mind has been implanted with the Index-Librorum-Prohibitorum — all the magical texts the Church has removed from circulation.