In Mitakihara, Madoka and Homura are hunting a witch. When Sayaka appears before them, she reveals to them the secrets she has learned about magical girls, as well as what has happened to Mami.
Iroha Tamaki is unable to recall the wish that made her a magical girl and starts to dream of a mysterious figure. When her partner, Kuroe, tells her of a rumor that magical girls can be saved in Kamihama City, they try to look into it.
Yachiyo searches for the Magius' headquarters alone while still grieving the loss of Iroha and the others. On one of the days of her search, she comes across a familiar face.
Yachiyo and Kuroe find Iroha in the Rumor of the Eternal Sakura, but her doppel suddenly emerges without warning. Before Yachiyo and Kuroe can react, they are trapped and teleported to the world of Iroha's dreams.
Iroha recalls the memories of her sister, Ui, and returns to Kamihama in search of clues of her whereabouts. While there, she meets a trio of magical girls named Momoko, Rena and Kaede, who are searching for what they believe is a Witch.
After Kaede is abducted, Momoko and Rena formulate a plan to get her back with Iroha tagging along to help. Also joining their group to help them is Yachiyo, the girl that Iroha encountered previously on her first visit to Kamihama.
Iroha and Yachiyo confirm the rumor of the Séance Shrine and see the people they wished to meet. Unfortunately, they turn out to be impostors and are attacked by the monster of the shrine. As they fight, Iroha's Soul Gem begins to darken.
Iroha learns that Nemu is looking for her. Believing that Nemu remembers her, Iroha asks Kuroe to take her and Yachiyo to Hotel Faint Hope. When they arrive at the entrance, however, the Amane sisters appear and the group is split apart.