Iroha Tamaki, a Student in Takarazaki City, has been battling Witches as a Magical Girl. However, Iroha can't seem to remember the wish she made when she became a Magical Girl. One day, she hears a rumor from another Magical Girl, Kuroe, that Magical Girls can be saved if they go to Kamihama City. During a battle with a Witch, Iroha unexpectedly finds herself in Kamihama but…

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.

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.

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.

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.