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…

Felicia was asked to join the Wings of the Magius, an organization that works within the shadow of rumors. She betrays Iroha and her friends and joins them. Kyoko is also invited by the Wings of the Magius and decides to join the organization. Iroha and company track Felicia down to an underground waterway, where the Wings of the Magius lurk. When the good luck count from the Lucky Owl Water reaches zero, it is said that unimaginably bad luck will befall whoever drank it.

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.

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.