A Magi is a magician whose inclination toward magic is so immense that they can be said to shape the world. With their significant influence, each Magi chooses a worthy candidate to become a king, then helps them conquer strange labyrinths called Dungeons and acquire the power of mythical djinns within. Above all else, the Magi supervises their elected representative as they build a country that might one day bring the world to its knees. Aladdin is a young Magi wandering the world in search of his true self. However, his journey is not a lonely one, as he is accompanied by his friend and mentor Ugo—a djinn he summons using his flute. In his travels, Aladdin also befriends Alibaba Saluja and guides him to a nearby Dungeon. With this newfound friendship, they begin an epic adventure across the world, witnessing various irregularities that seem more frequent than ever.

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...