Season 1: The mystery of the Level Upper reveals that teacher Harumi Kiyama linked thousands of student brains into a biological supercomputer to discover a cure for her former students (the Child Errors), who were deliberately placed into comas during unmonitored human experiments. Mikoto defeats Kiyama, and later in the Poltergeist arc, Judgment unites to thwart Therestina Kihara Lifeline, successfully liberating the comatose children.
Season 2 (Railgun S): Mikoto uncovers Project Radio Noise (the Level 6 Shift Project): researchers determined that Accelerator will evolve into the first Level 6 esper by killing 20,000 clones of Mikoto in pre-calculated combat scenarios. Horrified by the brutal murders of clones like Misaka 9009 and 9982, Mikoto attempts sabotage and battles ITEM. Driven to despair, she prepares to commit suicide against Accelerator to disrupt the calculation data. Touma Kamijou intervenes, defeats Accelerator using his Imagine Breaker, disproves the simulation's certainty, and permanently halts the project, freeing the surviving 9,969 Sisters.
Season 3 (Railgun T): During the Daihasei Festival, Gensei Kihara uses the Exterior brain network and a virus injected into Misaka 10032 to force Mikoto into an involuntary Level 6 Shift, mutating her into an apocalyptic entity. Misaki Shokuhou tricks and defeats Kihara using memory traps, while Touma and Sogiita Gunha hold off Mikoto's dragon transformation until Touma neutralizes the energy core. In the Dream Ranker arc, Mikoto battles a rogue cyborg possessing Ryōko Kuriba’s split soul using an electromagnetic iron-sand kaiju, ultimately convincing the Doppelgänger of its existential worth before it peacefully dissolves.