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.

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.

After celebrating their victory against Al-Thamen, Aladdin and his friends depart the land of Sindria. With the end of the battle, however, comes the time for each of them to go their separate ways. Hakuryuu and Kougyoku are ordered to go back to their home country, the Kou Empire. Meanwhile Aladdin announces he needs to head for Magnostadt—a mysterious country ruled by magicians—to investigate the mysterious events occurring in this new kingdom and become more proficient in magic. For their part, encouraged by Aladdin's words, Alibaba and Morgiana also set off in pursuit of their own goals: training and going to her homeland, respectively. Magi: The Kingdom of Magic follows these friends as they all go about their separate adventures, each facing their own challenges. However, a new threat begins to rise as a great war looms over the horizon...

Though Sayaka Miki's wish was fulfilled, the unforeseen consequences that came with it overwhelm her, causing her soul gem to become tainted as she succumbs to despair and eventually loses her humanity. Homura Akemi reveals to Kyouko Sakura and Madoka Kaname the ultimate fate of magical girls: once their soul gem becomes tainted, it transforms into a Grief Seed, and they are reborn as witches—a truth Homura learned only through repeating history countless times in a bid to prevent Madoka's tragedy. Kyuubey only compounds their despair when he confesses his true intentions: to harness the energy created from magical girls and use it to prolong the life of the universe. As the threat of Walpurgisnacht, a powerful witch, looms overhead, Homura once again vows to protect Madoka and the world from a grim fate. Caught between honoring Homura's wish and saving the world, which one will Madoka choose in the end? Mahou Shoujo Madoka★Magica Movie 2: Eien no Monogatari is a story of inescapable destiny, and an unlikely hero who could change it all.