Season 2

Haru'ue joins Saten and Uiharu on a trip to the Garden of Learning to see Misaka and Shirai, as well as to do some shopping. They later go to visit Edasaki in the hospital, where she is undergoing physical therapy, when things take an unexpected twist.

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.

In high spirits, Misaka joins the other girls for a day of shopping at Seventh Mist, where she helps the others with their shopping, as well. Misaka spends another day playing with children. One of Misaka's clones goes through the phases of her training.

Finding herself face-to-face with a clone of herself, Misaka ends up helping her get a cat out of a tree, sharing ice cream cones, and having tea with her. It isn't until later that Misaka discovers the true, sinister project that calls for her clones.

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.

Misaka manages to sabotage most of the experimental facilities remotely before she is cut off, leaving her to deal with the rest in person. Shirai resolves to help Misaka by doing her part to be more vigilant at work, but risks shutting the others out.

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.

Having realized who Misaka is, Mugino decides to give her a run for her third-place ranking. When Frenda mistakenly leaves her doll-bombs behind while heading to the other facility, Misaka collects them and uses them to supplement her diminished powers.

Misaka and Kamijo meet again at the malfunctioning vending machine in the park, where Shirai mistakes him for being Misaka's boyfriend. Misaka becomes shaken when she bumps into another Misaka clone, and learns that the experiments are still ongoing.

Misaka sets out on one last mission to put a halt to the experiments by destroying the supercomputer Tree Diagram. Meanwhile, Kamijo runs into Misaka's clone #10032 again, and the two of them decide what they should do about a stray kitten she has found.

Thwarted in her attempt to sabotage Tree Diagram, Misaka takes her frustration out on a nearby lab that is part of the project. Meanwhile, Accelerator and #10031 carry out their experiment, while Kamijo searches for Misaka's missing sister.

While Shirai frets about Misaka staying out again all night, she receives a visit from Kamijo, who manages to find Misaka's documents about the project. Kamijo catches up with Misaka on a bridge, where he tries to talk her out of doing anything rash.

Kamijo races to the scene of the experiment, only to find that it has already started. Kamijo calls out Accelerator, who takes him to be yet another challenger to his position, until for the first time, as Misaka watches on, he gets his nose bloodied.

Misaka stands up for clone #10032, declaring that she is doing so because they are sisters. The next day, the two of them spend time in a park, where 10032 asks her for a special favor. Later, Misaka has difficulty trying to express her thanks to Kamijo.

With the end of summer vacation approaching, the girls plan a study session at Saten's apartment to catch up on homework. Everyone is to bring an ingredient for a potluck stew party, but most have trouble deciding what to buy, leading to some surprises.

Edasaki is due to be discharged from the hospital, and it is learned that she will be living with Haru'ue. The move is bittersweet for Uiharu, who is losing her roommate, but she feels it is for the best. Meanwhile, a new movement is afoot in the city.

Febri takes an instant liking to Saten, and is warm to everyone except for Misaka, much to her chagrin. At Judgment, Uiharu is unable to find any information on who Febri is, so arrangements are made to admit her into an orphanage as a "Child Error."

As Yomikawa takes over investigating the runaway security robots, Konori invites the whole gang out to take in a bath at a bathhouse. On their way home, a number of detours lead them to a confrontation with yet another, much more dangerous runaway robot.

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.