Accompanying Madoka Kaname and Sayaka Miki to Kamihama City to rescue their friend Mami Tomoe, Homura Akemi harbors new hopes after hearing that magical girls could be saved there.

Unfortunately, Kamihama is currently facing a turbulent period, as the conflict further escalates between the Wings of Magius and those opposing its questionable actions. Amid these troubling circumstances, Yachiyo Nanami feverishly searches for the missing Iroha Tamaki, suspecting the magical girl organization to be responsible for her disappearance. To Yachiyo's surprise, help arrives from where she least expects it.

With perturbing events developing at an alarming speed, companions old and new come together in a combined effort to foil the Wings of Magius' devious schemes.