Iroha decides to investigate Kamiahama City’s rumors in order to find clues about her missing sister, Ui. Mitama introduces Iroha to Tsuruno, the daughter of the owner of a Chinese restaurant called Banbanzai. Tsuruno asks someone who is familiar with the rumors to help investigate, but Yachiyo is the one who shows up at the meeting spot. Tsuruno says Yachiyo is knowledgeable about the rumors of Kamihama City. The three suspect that the Séance Shrine may have something to do with Ui’s disappearance…

At the Séance Shrine, Iroha wrote her sister's name, Ui, and Yachiyo wrote the name of her former best friend, Mifuyu, on votive plaques. As if to confirm the truth of the rumor, Ui and Mifuyu appear, but they are twisted imposters of their loved ones. Iroha and Yachiyo are attacked by the fake Mifuyu and the master of the Séance Shrine, a Horse Monster, and find themselves in a bind that threatens to end their lives. Iroha's Soul Gem gets cloudy, making her slowly lose consciousness. What sort of transformation will she undergo?

Iroha moves into Mikazuki Villa and transfers to Kamihama City University Affiliated School. She discovers that even though Kaede goes to the same school, she is unable to contact her. Iroha has a hard time getting used to her new surroundings, so when she sees that Rena doesn't have many friends in class, they decide to eat lunch together on the rooftop. Iroha is still gathering information about various rumors, and Rena tells her about the rumor of the Invisible Girl and Endless Solitude. Tsuruno hears about the rumor of the Radio Wave Girl from a regular at Banbanzai and tells Iroha about it.

Iroha is convinced that all rumors are connected, so she decides to reply to the spam messages that are being repeatedly sent to her. The one who has been sending the texts calls herself Ai, and she asks Iroha to come to Endless Solitude to delete her existence. However, Sana Futaba, who is a captive in Endless Solitude, seems to be satisfied with her life there.

Ai decides to disappear in order to free Sana. Alina is infuriated by the destruction of Endless Solitude and goes into full attack mode against Iroha and her friends. They find out that the Magius have been using the Uwasa's territory to confine and raise Witches. Iroha and company fight an uphill battle, but Mami and Mifuyu appear on the scene to put an end to Alina’s rampage.

A student at Mizuna Girls' Academy, Tsukuyo, is hiding the fact that she is a member of the Wings of the Magius. Iroha goes to see Tsukuyo and asks to be introduced to Nemu Hiiragi, a friend of Iroha’s sister, Ui. Tsukuyo promises to Iroha that she will talk to Mifuyu about the matter. Sana has gotten accustomed to living at Mikazuki Villa, and suggests to everyone that they surprise Yachiyo with a gift, but…

With Yachiyo in low spirits, Iroha and company leave her behind and head for the Memory Museum. Touka Satomi, a friend of Iroha’s sister, Ui, awaits them there to give them a lecture about the truth of Magical Girls. Yachiyo’s past memories give her a push, and she decides to go find Iroha. However, at that very moment Iroha is already in the midst of a "vicarious practical learning" course prepared by the Magius.

Iroha refuses to join the Magius. When she and Yachiyo meet up, she is eager to go search for Tsuruno and the other girls. However, Yachiyo believes that her wish brings tragedy to those around her and tells Iroha that she is disbanding the team. The Memory Museum begins to collapse. Iroha and Yachiyo try to escape, but Mami, who has become an entirely different person, attacks them.