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.
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.
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.
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.
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.
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.
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.
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.
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 her.