Mikoto Misaka and her friends are back, investigating rumors across Academy City. Soon, Mikoto discovers something terrifying: horrific experiments are taking place throughout the city, involving the murder of thousands of espers. Moreover, these espers are far from just ordinary people: they are clones of Mikoto herself. Feeling responsible for their treatment, she sets off to put an end to the experiments; however, the forces opposing her are much more dangerous than she anticipated, and Mikoto finds herself up against some of the most powerful espers imaginable. Toaru Kagaku no Railgun S continues the story of the Railgun as she desperately fights to put an end to the inhuman experiments that she believes she helped cause, her life dragged deep into despair in the process. There's never a dull moment in Academy City, but no one ever said all of them would be pleasant.

Since ancient times, shrine maidens who wield swords have been exorcising aratama, strange existences that threaten the human world. These young women who wear school uniforms and a sword are called Toji, and they serve as an official unit within the police force as a special religious service police squad. The government authorizes the Toji to wear swords and serve as government officials, and the government has set up five schools throughout the country for the girls to attend. In the spring, the five schools send their best Toji to compete in a tournament. As the tournament comes closer, all of the representatives rigorously train themselves in order to get stronger and improve their skills. (Source: ANN)

Academy City stands at the forefront of scientific and technological progress, best known for their development of espers: those capable of wielding superhuman abilities that alter the rules of reality. The most powerful among them are the Level 5s, and the one known as Accelerator reigns supreme, even after being weakened by a severe brain injury. By his side is the young girl known as Last Order, whom despite his cold demeanor, he holds closely and vows to protect at all costs. Though Accelerator may be recovering from his injury, the dark side of Academy City never rests, and so he finds himself unwillingly caught up in the midst of a new conflict. When a mysterious young woman approaches Accelerator in pursuit of Last Order, the highest-ranked esper is confronted by a venomous organization that has taken root in Anti-Skill, Academy City's peacekeeping organization. With dangerous forces on the move that threaten to put Last Order and her sisters at risk, the self-proclaimed villain prepares to step into the darkness once again.

The Daihasei Festival has begun, and that of course means that Tokiwadai Middle School—a prestigious all-girls' middle school—is competing too. Despite the participation of the Ace of Tokiwadai, Mikoto Misaka, the other students who are participating are still putting their utmost effort into winning, no matter how impossible the feat may seem against her overwhelming might. However, not all is fun and games. Due to the festival, Academy City opens to the outside world, and various factions have begun plotting ways to infiltrate the city. Misaka appears to be on their radar, and as the festival proceeds, people lurking from the shadows begin to emerge... Toaru Kagaku no Railgun T brings back the Tokiwadai Ace and her friends as they dive deeper into the dark side of Academy City. From terrorist attacks to ruthless underground projects, anything is possible in this city.