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…

Iroha remembers that her wish was to cure her younger sister, Ui’s, illness; however, there is no sign of Ui’s existence in her life. She goes to Kamihama City to find clues about her, but is attacked by a Witch and subsequently saved by a trio of Magical Girls, Momoko, Rena, and Kaede. There is a rumor going around about the Friendship Ending Staircase at Rena and Kaede’s school. Momoko and the others believe that a Witch is involved in the rumor, so they’ve been investigating it, but…

Rena wrote Kaede's name on the Friendship Ending Staircase. Kaede apologizes to Rena, but she is kidnapped by the Chain Monsters, confirming that the rumor about the staircase was true. In order to find Kaede and bring her back, Momoko and her companions come up with a strategy to lure out the Chain Monsters. Yachiyo has joined the group after being asked by Momoko to help them. Yachiyo claims that Iroha will hinder the operation and refuses to let her participate in the battle with the Chain Monsters.

Iroha decides to investigate Kamiahama City’s rumors in order to find clues about her missing sister, Ui. Mitama introduces Iroha to Tsuruno, the daughter of the owner of a Chinese restaurant called Banbanzai. Tsuruno asks someone who is familiar with the rumors to help investigate, but Yachiyo is the one who shows up at the meeting spot. Tsuruno says Yachiyo is knowledgeable about the rumors of Kamihama City. The three suspect that the Séance Shrine may have something to do with Ui’s disappearance…

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 wanders into Kosho Ward in Kamihama City. On the street, she is offered some Lucky Owl Water, which is said to bring good fortune, and without much thought, takes a sip. Another Magical Girl named Felicia also happens to drink the Lucky Owl Water. Wherever they go together they have extremely good luck. They have such good luck, in fact, that Iroha finds it a little strange. Felicia makes a living as a mercenary, and offers her services to Iroha to help find Ui, 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.

Iroha moves into Mikazuki Villa and transfers to Kamihama City University Affiliated School. She discovers that even though Kaede goes to the same school, she is unable to contact her. Iroha has a hard time getting used to her new surroundings, so when she sees that Rena doesn't have many friends in class, they decide to eat lunch together on the rooftop. Iroha is still gathering information about various rumors, and Rena tells her about the rumor of the Invisible Girl and Endless Solitude. Tsuruno hears about the rumor of the Radio Wave Girl from a regular at Banbanzai and tells Iroha about it.

Iroha is convinced that all rumors are connected, so she decides to reply to the spam messages that are being repeatedly sent to her. The one who has been sending the texts calls herself Ai, and she asks Iroha to come to Endless Solitude to delete her existence. However, Sana Futaba, who is a captive in Endless Solitude, seems to be satisfied with her life there.

Ai decides to disappear in order to free Sana. Alina is infuriated by the destruction of Endless Solitude and goes into full attack mode against Iroha and her friends. They find out that the Magius have been using the Uwasa's territory to confine and raise Witches. Iroha and company fight an uphill battle, but Mami and Mifuyu appear on the scene to put an end to Alina’s rampage.

A student at Mizuna Girls' Academy, Tsukuyo, is hiding the fact that she is a member of the Wings of the Magius. Iroha goes to see Tsukuyo and asks to be introduced to Nemu Hiiragi, a friend of Iroha’s sister, Ui. Tsukuyo promises to Iroha that she will talk to Mifuyu about the matter. Sana has gotten accustomed to living at Mikazuki Villa, and suggests to everyone that they surprise Yachiyo with a gift, but…

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.

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.

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.

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.