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.

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...

The kingdom of Kouka is blessed with a beautiful princess whose childlike innocence charms all who come across her. Named Yona, she has grown up sheltered in the royal palace, shielded from any danger that may befall her. However, all good things must come to an end. Yona's perfect world comes crashing down when a heinous act of treason threatens to erase all that she holds dear, including her birthright as the princess of Kouka. Left with no one to trust but her childhood friend and loyal bodyguard Son Hak, she is forced to flee the palace. Faced with the perils of surviving in the wild with a target on her back, Yona realizes that her kingdom is no longer the safe haven it once was. Free from the shackles of naivety, Yona vows to do everything in her power to become strong enough to crush her enemies. With Hak by her side, she must piece together the remains of an ancient legend that might be the key to reclaiming her kingdom from those who conspired to steal it from her.

Maomao, an apothecary's daughter, has been plucked from her peaceful life and sold to the lowest echelons of the imperial court. Now merely a maid, Maomao settles into her new mundane life and hides her extensive knowledge of medicine in order to avoid any unwanted attention. Not long after Maomao's arrival, the emperor's infant children inexplicably begin to experience grave symptoms—almost as if a curse has been cast. The curious Maomao easily solves the mystery and, to remain out of the limelight, attempts to leave an anonymous tip. Unfortunately, the dashing and perceptive eunuch Jinshi sees through it and manages to single her out. In recognition of her talent, Maomao is promoted to lady-in-waiting for the emperor's favorite concubine, Gyokuyou. As Maomao continues to remedy the numerous ailments afflicting the imperial court, her pharmaceutical expertise quickly proves indispensable.