"A Certain Scientific Accelerator" is a spin-off of the "A Certain Magical Index" series, centering on Accelerator, one of the most powerful espers in Academy City. The story begins shortly after the events of the "Sisters Arc," where Accelerator, having renounced his violent past, is recovering from severe injuries sustained in a battle. His life takes a new turn when he encounters Last Order, a clone of Misaka Mikoto and the central control unit for the Misaka Network. Despite his initial reluctance, Accelerator becomes her protector, forming an unlikely bond with the childlike clone.

The narrative escalates when a mysterious organization called DA (Disciplinary Action) emerges, targeting Last Order to exploit her connection to the Misaka Network. Accelerator, though physically weakened, uses his unparalleled esper abilities to defend her. The conflict deepens as DA's true motives are revealed: they aim to destabilize Academy City by manipulating the Misaka Network and its clones. Accelerator's journey intertwines with other characters, including Esther Rosenthal, a necromancer seeking to resurrect her mentor, and Yomikawa Aiho, a law enforcement officer who provides support.

The series explores themes of redemption, morality, and the consequences of scientific experimentation. Accelerator's character development is central, as he grapples with his past actions and seeks to atone for them by protecting Last Order and others. The plot is driven by high-stakes battles, intricate conspiracies, and the ethical dilemmas surrounding the creation and treatment of the Misaka clones. The interplay between science and morality is a recurring motif, with Academy City serving as a backdrop for the clash between technological advancement and human values. The series maintains a balance of action, emotional depth, and philosophical inquiry, making it a compelling addition to the "A Certain" universe.