Thirty years ahead of the rest of the world scientifically and home to millions of students enrolled in the esper development program, Academy City never sees a dull moment. Here, espers are given one of five power levels, the highest of which consists of only seven members. Mikoto Misaka, a middle school electromaster, ranks third among these individuals, and is known as "The Railgun."

In a city known for housing extraordinary individuals, it comes as no surprise that extraordinary things tend to happen. Recently, makeshift bombs disguised as everyday objects have been ominously finding their way into public areas. Mikoto's best friend, Kuroko Shirai, has been investigating the case as a member of the student-based disciplinary committee Judgement. As more and more of these incidents come to light, it becomes apparent that a hidden darkness exists within Academy City, one that may not only impact Mikoto and her friends, but also the fate of the city itself.