When Hanako returns to school after a day of absence, she finds it in a state of consternation, as the latest edition of Koharu’s school newspaper has published stolen nude photographs of an unidentified co-ed. Though able to provide a convincing alibi, Koharu is nevertheless blamed for the stunt, and the newspaper club is disbanded on the spot. Enraged by the staff’s treatment of their newfound friend and convinced of her innocence, Hanako and Shinju head to the library, where Hanako manages to smuggle the laptop Koharu used for her newspaper writing out of the school, planning on it over to her lawyer mother. Meanwhile, Koharu starts an investigation of her own, believing the stunt to be a set up by the same person that tried to make her publish misinformation. She manages to identify the girl in the scandalous pictures as one Niko Segawa, an upperclassman in the school’s track and field club.

Before Koharu can track her down, however, Rui Tomatsu pays Niko a visit and reveals herself to be the culprit behind the leaked photographs, Invoking the friendship they apparently used to share, as well as a certain incident that forced Rui to leave the track and field club, Rui manages to manipulate Niko into collaborating on her plan to discredit Koharu. In the meantime, Hanako has started taking up training under Shinju’s sister Kohaku. As the two head out on a Witch hunt, they are joined by a Puella Magi named Yasu Matsushita. As Kohaku shows off her ability to summon a construct resembling her younger sister, which seems to have a will of its own, the trio vanquishes the Witch, with the newcomer seizing the Grief Seed. After the battle, Yasu reveals she too is a Mitakihara High student, but warns Hanako not to get too close to her at school before vanishing.

The next morning, Koharu herself learns about the troubles plaguing the school’s track club and begins to suspect it’s not just her whoever leaked Niko’s pictures may have a bone to pick with. Meanwhile, an increasingly more confident Hanako and her mother dig through the library laptop to find proof that the school indeed tampered with evidence in order to facilitate blaming the leaked photographs on Koharu, while Shinju strikes up conversation with Niko’s closest friends, two track club members named Chiemi Takahata and Akari Fueki. Though the two seem willing to share some information, Akari is felled by a spell of nausea as soon as she opens her mouth, causing Chiemi to cut the conversation short and escort her friend to the nurse’s office.

Eventually, Koharu, Hanako and Shinju manage to piece together the puzzle with what little hints they have — Rui Tomatsu used to be a member of the track and field club with Niko, Chiemi and Akari, and seems to be blackmailing her former friends in a ploy to ruin Koharu’s reputation. A conversation between Rui and Kyubey reveals the full extent of that blackmail — Rui has been using intimidation, deceit and the guilt her former friends feel about an incident that caused Rui to be expelled from the track club, in order to coerce them into making contracts with Kyubey on her behalf. In doing so, Rui dictates which wishes they are to make as a part of their contracts, all to put into motion a plan to enact revenge on the person she holds accountable for her expulsion: Koharu Shirahara.

Not to let Koharu’s issues distract her from her duties as a Puella Magi, Hanako ventures out on a Witch hunt, only to get attacked by Yasu Matsushita, the same girl who had saved her earlier. When Hanako reports on Yasu’s betrayal to Koharu, the two deduce that Kyubey and Rui must be working together somehow, and that Yasu is likely being blackmailed by Rui as well. Realizing their lives are into danger, Hanako tells Koharu she wants to come clean to Shinju about her double life as a Puella Magi — only to learn Shinju has already fallen into Rui’s clutches. Infuriated by her investigation into the track and field club, Rui and her associates torture Shinju into making a contract with Kyubey, However, when the creature tries to uphold its end of the bargain, things go awry, forcing Rui to retreat. Disappointed, Kyubey concludes that Shinju cannot become a Puella Magi as she does not have a soul, having lost it when her sister wished her back to life.

With the clock ticking, Koharu, Hanako and Shinju manage to find what they believe to be the leverage Rui has on her various victims — they discover Niko took the explicit selfies with the intention of selling them, and learn Rui once convinced the school not to punish Yasu for assaulting a classmate. Intending to bring the bully down, the three girls put their plan into motion, when the entire student body is told to assemble in the auditorium to listen to a public apology Koharu has been made to recite. As Koharu makes a scene on stage, Shinju pickpockets Rui’s phone and uses it to reveal Niko’s secret to the entire school. Realizing she has nothing to blackmail Niko with any more, Rui triggers the fire alarm, causing a major commotion. Amidst the chaos, Niko notices Shinju with Rui’s phone, and chases after her in a blind rage. As the student body evacuates, Hanako rushes to Shinju’s aid and manages to take Niko down, only to get attacked by Yasu.

Koharu, in the meantime, has been left alone in the auditorium with Rui. When Koharu confronts the bully with the results of her investigation, Rui finally reveals to Koharu her motives — revenge for the aspiring journalist for reporting on Rui using a performance-altering inhaler during a track meet — a fact Koharu doesn’t even remember happening. Rui explains she needed the inhaler for her asthma, and had been forced by her mother to keep taking it despite the risk, but Koharu dismisses this as an excuse Rui invokes to justify what is little more than bullying. When Koharu claims Rui no longer has any more leverage to bend others to her will. Rui scoffs and summons an entire gang of Puellae Magi, revealing that Niko and Yasu are far from the only two girls she has under her control. In fact, the entire track club — including Niko’s friends Chiemi and Akari — has fallen victim to Rui’s machinations, as punishment for failing to support Rui when she was expelled from the team.

Meanwhile, Hanako continues to clash with Yasu, while an incapacitated Niko opens up to Shinju about her anxieties, her motives for working with Rui, and for taking the compromising pictures in the first place. Realizing that Yasu and Niko are failing to properly dispose of Hanako and Shinju, Rui commands her other subordinates to finish them off, breaking Koharu’s jaw to silence her when she protest and forcing Hanako and Shinju to retreat. Niko chooses to stay behind to protect the two, having her own bones to pick with the other track club girls, but is killed in the process. Horrified at the track club girls’ willingness to kill one of their own, Hanako and Shinju manage to flee the school building. At the same time, Koharu makes use of the distraction to outwite Rui and slip away. As the three make their escape, Rui is forced to retreat upon learning that Niko is dead, and the police are on their way to the school.