Rumor has it that if a young girl strikes a bargain with a white fairy, it will grant any wish her heart desires. However, in exchange, she will become a magical girl and must put her life on the line to slay fearsome and ferocious witches. Iroha Tamaki, a kind-hearted middle schooler from Takarazaki City, is living proof that these rumors are true. Armed with a magical crossbow and the ability to heal injuries, Iroha seeks out the labyrinths where witches hide and defeats them before they can prey on humans. Yet Iroha has no memory of her wish, and even Kyuubey, the white fairy himself, seems to have no idea what Iroha requested of him. One day, Iroha hears rumors of a city where "magical girls can be saved," and finds herself on a sunset train to Kamihama City. Unfortunately, she discovers that the witches in Kamihama are far more powerful than usual. After veteran magical girl Yachiyo Nanami is forced to save her, Iroha vows to never return. But when a chance encounter with a tiny Kyuubey seems to trigger distant memories, Iroha is compelled to investigate the mysterious city despite the danger.

After a daring escape from the Memory Museum, Sayaka Miki returns to Mitakihara City with unsettling news. Troubled by what she has learned, Sayaka reveals to Madoka Kaname and Homura Akemi the whereabouts of Mami Tomoe—but more importantly—the disturbing truth behind the existence of magical girls. Despite knowing the cruel fate that awaits them, the three quickly resolve to work together and save Mami once and for all. Meanwhile in Kamihama City, Yachiyo Nanami hunts various "rumors" in search of Hotel Fendt Hope, the headquarters for the Wings of Magius. The magical girl organization is Yachiyo's only lead in finding Iroha Tamaki, whose disappearance remains shrouded in uncertainty. Determined to reunite Team Mikazuki Villa, Yachiyo swears to destroy the Wings of Magius and put a stop to their insidious plans. Amid the turbulent situations, a calamitous threat approaches, presenting a dire conflict set to jeopardize the entire world.

The desperate battle in Kamihama City continues to intensify. With Walpurgis Night changing course for Mitakihara City, all eyes shift toward Embryo Eve—an artificial being, currently dormant, that can allegedly liberate magical girls from their destinies. As the Wings of Magius grow dangerously close to executing their plan, Iroha Tamaki's last chance to stop the organization is quickly fading. Despite the dwindling odds, lingering hope for the dawn of a better future invigorates her final endeavor, while also uncovering memories of a story tampered with by the hands of fate.