After dreaming of her past, Misaka sets out for a day of shopping, but when Kuroko suggests a shortcut, they find an envelope with a cash card in it--one of many placed throughout town. Elsewhere, Saten thinks she sees someone who looks like Misaka.

Rumors swirl about that Misaka is the template for a project to produce Level 5 clones. When Nunotaba refers to her as the "Original," Misaka decides to check her out, and learns that she worked at the hospital where Misaka submitted her DNA map.

Misaka lashes out at Accelerator, but is left frustrated. She realizes the full breadth of the situation she has become involved in, and feels responsible for allowing it to happen. Nunotaba discusses the ramifacations of the clones' existence with Misaka.

The members of the underworld organization ITEM finish one mission, and are called in to defend the remaining facilities. When Misaka tries to infiltrate one building, she encounters Item member Frenda. Meanwhile, Nunotaba drops in at the other facility.

As Misaka continues her way into the research facility, she and Mugino play a game of cat-and-mouse. Meanwhile, at the other facility, Nunotaba sneaks into a control room, planning to disrupt the experiment by adding a new factor to the Misaka Network.

With the revelation that Febri is synthetic, Misaka is determined to find whoever built her, and have them fix her. The investigation is stalled on all fronts, even with the help of her friends running down leads, until help comes from a surprise source.

Therestina reluctantly provides Misaka with the clues she needs to find the group behind Febrie's secret. With Kongo's help, the girls identify Aritomi as the man they are pursuing, and find out more about him and his company, the STUDY Corporation.

Aritomi reveals his motivations for STUDY's project to Misaka. She also learns about Nunotaba's plight, and some of the details concerning what STUDY has planned at the Reach Assembly the next day. Will she be able to escape and put a stop them?

Shirai, Konori, Kongo and friends, and Uiharu and Saten confront the powered suits at the four Assembly sites, where they soon receive backup. Misaka and Febrie move to take on Aritomi directly, but he has one final surprise up his sleeve for them.