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 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.

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…

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.

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.

The Magical Girls rush to Iroha while fighting against Uwasa of the Soldier Bear. The Amane sisters also stand in their way, but Mifuyu keeps them in check. "The plans of the Magius have failed." Meanwhile, Iroha and Touka regain the memories that Nemu's power took from them. Touka is happy to be reunited with Iroha but can’t recall why they became enemies in the first place. Nemu tells Touka why she had been hiding the truth until now. Now, they see the promise they made with Ui in a new light.

Iroha grieves about the battles that have been fought so far and figures she couldn’t save anyone in the end. Kyubey thanks Iroha and says that her hope caused everyone to fall into despair. The despair of Magical Girls is what Kyubey has been seeking all along. All the while, Iroha’s Doppel continues tormenting her. As a result of Iroha’s interference with the Magius, more Witches will be born. On the brink of despair, Iroha hears a familiar voice call out to her.