Academy City's espers are divided into six levels, with "Level 0" representing no power and "Level 5" being overwhelmingly powerful. Only seven out of the millions of espers in the city have reached Level 5, and the top-ranked one is known as Accelerator.
Toaru Kagaku no Accelerator follows the story of this strongest Level 5, who sacrifices much of his power to protect the cheerful Last Order. After recovering in the hospital and living a relatively peaceful life, Accelerator unexpectedly saves Estelle Rosenthal, a mysterious girl carrying a photo of Last Order. However, this incident drags Accelerator into a conflict with a malevolent organization called Disciplinary Action. Their goal is to use Last Order for a dangerous mission, and now they are in pursuit of the young girl. It is up to the world's most powerful esper and his new companion to protect Last Order and defend Academy City from the organization's plans.