Arc 1
A creature named Kyubey has the power to grant girls a wish, but in exchange they must become magical girls and fight against creatures known as Witches. Soon, a rumor begins to spread among magical girls that they can be saved from their duty if they go to Kamihama City.
Iroha Tamaki, a girl who has forgotten the wish she made to become a magical girl, encounters a smaller Kyubey named Lil' Kyubey and remembers that she had wished to cure her younger sister Ui of her illness. After realizing that all evidence of Ui's existence has disappeared, she travels to Kamihama City in search of answers, where she meets Yachiyo Nanami, a veteran magical girl. Uncertain of how to proceed in her search for Ui, Iroha decides to investigate rumors in the hopes that they may provide clues to her whereabouts, and learns that they manifest as uwasa, creatures that resemble witches and have their own labyrinths. Over time, Iroha forms her own group of magical girls, consisting of herself as well as Yachiyo Nanami, Tsuruno Yui, Felicia Mitsuki, and Sana Futaba. However, her group comes into conflict with the Magius, a mysterious organization of magical girls who are dedicated to the "salvation" of magical girls and the protection of the uwasa. It is led by Alina Gray, Nemu Hiiragi, and Touka Satomi; the latter two were Ui's close friends, but now have no memory of her.
After Iroha and her group defeat several uwasa across Kamihama City, the Magius decide to take drastic measures. Mifuyu, a senior member and Yachiyo's former friend, orchestrates a plan to convince Iroha's group to join the Magius. She invites them to a lecture where they are informed about the true nature of magical girls; their soul gems are directly connected to their lives and they are fated to become witches themselves. Mifuyu also informs them that the Magius created the doppel system, which essentially circumvents their fate but is only in place in Kamihama City; as such, they plan to extend it across the entire world. Iroha disagrees with the group's methods and refuses to join them, but Felicia, Tsuruno, and Sana are brainwashed into joining. Yachiyo, who did not attend the lecture but was aware of the truth about magical girls, relents after learning that Iroha's group has been essentially been disbanded because of Mifuyu's actions, but Iroha helps her regain her resolve.
The Magius leaders decide to resort to more extreme methods, such as brainwashing their own members, causing a disillusioned Mifuyu to defect from the group and covertly dispel Felicia and Sana's brainwashing. Tsuruno is fused to an uwasa to harvest energy from people, but Iroha's group manages to return her to normal and meet up with Mitama Yakumo, planning to gather the city's magical girls at her place for their safety.
Kamihama City's magical girls head to the Magius' headquarters, which is inside an uwasa's labyrinth, to fight them head on and learn that they plan to lure the witch Walpurgisnacht to the city to have it fight against their creation, known as "Eve", in order to gather enough energy to expand the doppel system. Iroha learns that Eve and Ui are one and the same and manages to convince Nemu and Touka of Ui's existence. Alina unleashes Eve upon Kamihama City as planned and its magical girls regroup at the city's center to stop both Eve and Walpurgisnacht. Iroha successfully returns Ui to normal and Walpurgisnacht is finished off by a combined attack from Yachiyo and Iroha.
