Rena wrote Kaede's name on the Friendship Ending Staircase. Kaede apologizes to Rena, but she is kidnapped by the Chain Monsters, confirming that the rumor about the staircase was true. In order to find Kaede and bring her back, Momoko and her companions come up with a strategy to lure out the Chain Monsters. Yachiyo has joined the group after being asked by Momoko to help them. Yachiyo claims that Iroha will hinder the operation and refuses to let her participate in the battle with the Chain Monsters.

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 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…

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.

Madoka and Homura fight an uphill battle against the Class Leader Witch. When the Witch’s minions attack Madoka, Homura stops time and uses a gun to save Madoka. However, the appearance of a mysterious girl takes Homura by surprise which breaks her spell to stop time. As the minions close in on Madoka, Sayaka returns from Kamihama City to save her from the impending crisis. Sayaka explains to Madoka and Homura what happened to Mami in Kamihama and the truth about the Magical Girls.

Yachiyo pursues Black Feather and the others to find Hotel Faint Hope, which is where the headquarters of the Magius is located. After battling the Uwasa of Peeking Castle Town, she walks through the shopping district where Uwasas have appeared before to find the entrance to Hotel Faint Hope. There, she meets a Magical Girl named Kuroe from Takarazaki City and small Kyubey, but Kuroe suddenly tries to run away. After chasing Kuroe, Yachiyo’s former best friend, Mifuyu Azusa, appears before her. Mifuyu explains that the methods of the Magius are necessary to prevent any more girls becoming victims like Iroha…

Yachiyo and Kuroe find Iroha inside the Labyrinth of the Uwasa of the Eternal Sakura. However, Yachiyo and Kuroe are swallowed by the Doppel of Silence that suddenly appears from Iroha’s body. When Yachiyo awakens, she finds herself at Mikazuki Villa eating breakfast with Tsuruno, Felicia, Sana, and Iroha, but Kuroe, who is not supposed to be there, is in the room with them. Yachiyo and Kuroe are baffled by the situation they are in, but they have a hunch that they are not in the real world, but in a dream world being shown to them by the Doppel of Silence. They are concerned about Iroha’s safety in the real world, so they do all they can to wake up Iroha in the dream.

Iroha embarks on a journey to find her friends from Mikazuki Villa. Kuroe is genuinely concerned about Iroha so she decides to tag along. Meanwhile, Felicia and Sana are working inside of the Magius as Black Feathers. Felicia proclaims that she will not return to Mikazuki Villa until she finds out how they can avoid becoming witches. Sana begins to question the actions of the Magius while she manages the people captured by the Uwasa,. Mifuyu, who is acting as a White Feather, finds herself in a predicament when she reunites with an unexpected person. Amidst the intricate tangle of everyone’s emotions, Touka announces her strategy to save all Magical Girls. What could it be?

The Magical Girls break into the headquarters of the Magius. After Iroha and Yachiyo reunite, they meet up with Madoka and the other girls, but are confronted by Tsuruno Yui and Mami Tomoe who have become soldiers of the Magius. Mami and Tsuruno, who are being manipulated by another entity, begin attacking the Magical Girls. Iroha and Madoka are in a bind as they are unable to fight back. As a tactic, the Magius summon countless Witches to gather in Kamihama City. The largest ever Supercell is approaching and will hit Kamihama City in six hours. The true identity of the Supercell is actually Walpurgisnacht, the most sinister and evil Witch ever.

Tsuruno, who had merged with the Uwasa, is defeated, which triggers Touka from the Magius to direct her rage toward Iroha and her friends. Touka sends the Uwasa of the Soldier Bear army to attack them. Nemu is upset with Touka’s actions and at how things aren’t turning out the way she intended. Meanwhile, Iroha finds herself alone in a strange world. She is sitting in a seat in a theater where a Magical Girl named Mel is predicting the future. When Iroha sees Mel, she remembers the past events that Touka showed her at the Memory Museum.