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 hears about Nemu Hiiragi, the best friend of Iroha’s younger sister, Ui, from Kuroe. Iroha finds out that Nemu, who is also a member of the Magius, remembers her and asks Kuroe to take her to Nemu so they can talk. Iroha, Yachiyo, and Kuroe head to Hotel Fendt Hope, the headquarters of the Magius. When the trio arrive at Hotel Fendt Hope, they have an encounter with the Amane sisters. While Yachiyo distracts the Amane sisters, Iroha and Kuroe make their way into Hotel Fendt Hope to find Nemu, but they bump into Rena Minami and Kaede Akino, who are dressed as the Black Feathers.

Kuroe lets Iroha get ahead of her while fighting with Magius. Kuroe hears a whisper that puts her in a shock: “Did you forget about me?” At the same time, Iroha is hearing Ui’s voice. Felicia and Sana are confused about Magius’ plan. Sana has questions and explains her intent to Mifuyu, who seems to have given up on everything. Due to the plan, Yachiyo is after Iroha in Kamihama City, which is filled with a large number of Witches. While there, Yachiyo comes across a Magical Girl from Mitakihara City.

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.