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. Eighty percent 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 to 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 (no esper powers). Together, the four encounter several adventures in the exciting scientific town.
Special abilities occur among a small percentage of boys and girls in puberty. Yū Otosaka uses his power without others knowing, and lives a fairly normal, average school life. Before him suddenly appears a girl, Nao Tomori. Due to his meeting with her, the fate of special power-users will be exposed.
Rinka Urushiba is a normal high school girl, until she encounters a penguin and shoals of glowing fish swimming through the sky. She looses consciousness only to awaken with the power to move through inanimate objects. At first she thought it was a hallucination if it were not for Kyotaro Azuma who witnessed the event and who, incidentally, has the ability to teleport. They decide to use their powers to combat people who might use their powers for evil.