A Certain Scientific Railgun S

Something sinister is growing in Academy City. The shadows are filled with whispers of a project to clone one of the super-powered students known as espers. High-ranking master of electricity Mikoto Misaka laughs off these stories until she comes face to face with a copy of herself. The duplicates are real, and are being mass-produced from Misaka’s DNA, making each one of them a little piece of her.

These clones—her sisters—are being systematically murdered in a series of experiments designed to turn a sadistic killer into the strongest esper in history. Misaka vows to save her copies and destroy the project, but this might be one fight she can’t win alone.

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The second season is focused on The Sisters Arc. Lasting only a single volume in the Toaru Majutsu no Index light novels, it was later expanded greatly in the Toaru Kagaku no Railgun manga.
The arc focuses on the ordeals of Mikoto Misaka after discovering the existence of the Radio Noise sisters that are being used in the Level 6 Shift, an experiment where they are killed in order for the highest-ranking Level 5, Accelerator, to achieve Level 6.