Madoka y Homura luchan una dura batalla contra la Bruja Líder de su clase. Cuando los esbirros de la Bruja atacan a Madoka, Homura detiene el tiempo y utiliza un arma para ayudarla. Sin embargo, aparece una misteriosa niña que sorprende a Homura y rompe su hechizo para detener el tiempo. Mientras los secuaces de la Bruja encierran a Madoka, Sayaka regresa de la Ciudad de Kamihama justo a tiempo para salvarla. Sayaka les explica a Madoka y a Homura lo que sucedió con Mami en Kamihama, y revela la verdad acerca de las Chicas Mágicas.

It happened in the past… Iroha would go to the hospital daily and play with Ui, Touka and Nemu. The girls loved Iroha and looked forward to her visits. One day, the three girls create an Uwasa similar to an urban legend while playing. That way, if they died, the Uwasa they created would live on and remind Iroha of them. Iroha also created the “Uwasa of Eternal Sakura”, with the wish that the three girls will be discharged from the hospital without illness. And one day... Kyubey appears before Iroha.

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.

To fulfill their promise to Ui, Touka and Nemu set their plan in motion with Embryo Eve. Yachiyo desperately tries to stop them. As Alina watches events unfold, Kuroe is isolated and alone. And Kyubey is not far behind… Meanwhile, Iroha wakes up in her room at home. Everything looks the same as when Ui was still around. Finally, Iroha is reunited with Ui.