S-Processor Laboratories

S-Processor Laboratories is a research institute in Academy City that apparently deals with several medical-related sciences and technology. They also masquerade as an institute devoted to the research and cure of muscular dystrophy. In truth, the facility focuses on the creation of Sister clones of Misaka Mikoto, in order for Accelerator to attain SYSTEM for the Level 6 Shift.

S-Processor Cranial Nerve Application Analysis Laboratory
Nunotaba Shinobu most likely chose the facility because of its application, the inputting of information into the Sisters using Testament, which she had been involved in back with the Radio Noise Project, allowing her to use it as leverage to enter the facility. However, Shinobu did not count on Last Order being kept there.

S-Processor Pathology Analysis Research Laboratory
Following the wake of recent terrorist attacks by Mikoto, the supervisor of the Level 6 Shift, initiates a trap for the culprit, which he suspects to be an electromaster after they analyzed the pattern and method of attacks, although he cannot prove that Mikoto is behind it. With two facilities left in involved with the project, the supervisor decides to cut losses and transfer the experiments to other facilities, which would mean the rights of the experiment will be forfeited to the destination. In spite of this, Amai Ao protests, though the supervisor continues with plan regarding this, and the only remaining variable is to take down the invader. As such, ITEM's liaison is contacted in order to arrange ITEM to protect the facility from the mysterious invader. The specific order to ITEM was not to make a move unless the invader infiltrates the facility first, and not to inquire of the invader's identity.

Shizuri, the leader of ITEM, anticipates the danger of an inside job and sends Kinuhata Saiai into the S-Processor Cranial Nerve Application Analysis Laboratory while Frenda Seivelun is to face the invader head on. Mugino meanwhile, along with Takitsubo Rikou check another research facility if the invader would attack there.

Sisters Arc

 * Main article:Sisters Arc

Here in the facility, Frenda has set-up some traps, and predictably, Mikoto shows up to destroy the facility, all the while, the researchers and employees of the facility evacuate themselves and their projects and reports from the premises due to ensuing battle.

Erstwhile, Mikoto battles Frenda and her traps, both with and without her powers due to Frenda's trickery. Even though she is severely disadvantaged by her weary state after her nonstop nightly operations against the facilities involved with the Radio Noise project, Mikoto is able to corner Frenda, and tries to pry some information from her. She is however, soon rescued by the arrival of Shizuri and Rikou, who overwhelms Mikoto and forces her to retreat deeper into the facility, although, with Rikou's powers, she is tracked down and attacked with precision. Forced into a corners, Mikoto uses her powers on Shizuri's attacks to deflect it, and realizing that what she is facing is the 3rd level 5, orders Rikou and Frenda to retreat.

Immediately, Shizuri tracks down Mikoto and after some fighting, Mikoto manages to knock her unconscious. With Shizuri's defeat, Mikoto takes the time to destroy the remaining equipment in the facility. Shizuri however, returns to seek out her vengeance upon Mikoto, however, with Shizuri's hubris and Frenda's lackadaisical attitude towards her own traps, Shizuri is once again defeated. With that, Mikoto evacuates the ruined facility. However, Shizuri survives her defeat and extorts information from one the evacuating researchers for information regarding the project the facility is doing. Hither, Shizuri realizes that Mikoto is suffering a great deal due to her involvement in the experimentation of her clones, and leaves Mikoto to her own machinations instead of seeking revenge, as she sees that she would rather have Mikoto struggle in the darkness of Academy City.

Mikoto visits the facility the next day, and discovers that no one is within it, as well as the fact that the facility has become bankrupt and has stopped the project. This gives Mikoto somewhat a short sigh of relief as she tries to return to her normal life and runs into Touma once again.

Meanwhile, Shinobu infiltrates another part of the Cranial Nerve Application Analysis Laboratory as well. All throughout the battle between Mikoto and ITEM, Shinobu tries to install basic emotions into the clones network, in order for them to at least feel able to fear the despair of dying and allowing the researchers to realize that they are not merely lab rats, or at the very least move a certain someone’s (Accelerator) heart. However, despite her best efforts to whether Saiai's assaults on her, she fails in her mission, due to the intervention of clone 20001, and is captured by Saiai.