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.

The Earth lies darkened and deserted. Despite the best efforts of the film's heroine, Hikaru, the evil-filled castle of Cephiro has taken over the world and stands in the center of a lifeless Tokyo. Before the ice-witch Alcyone can take her revenge on Hikaru, she is rescued by Lantis, a young man who seals her into a magical maze where she is challenged to prove her powers while her friends are hunted down by Cephiro's warlocks. Fleeing through the silent city, Umi and Fuu must seek out the sleeping Mashin; godlike creatures that will fuse with them to form giant warriors of awesome destructive power. But the Magic Knights are afraid, untrained and alone... will even the Mashin be enough to save them from the evil acts of Cephiro? (Source: AniDB)

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...

Hikaru Shidou, Umi Ryuuzaki, and Fuu Hououji are strangers brought together by fate when they meet during a seemingly normal field trip to Tokyo Tower. Accompanied by a great flash of light, they hear a mysterious woman's plea to save Cephiro, and the junior high heroines are suddenly swept away by a giant flying fish. Afterwards, they arrive in an unknown land, where they encounter a man called Master Mage Clef. Clef informs the girls that they were summoned by Princess Emeraude to fulfill their destinies as Magic Knights, restoring peace and balance in Cephiro. The formerly lively and peaceful land has been in disarray ever since High Priest Zagato imprisoned the princess, who acted as Cephiro's pillar of stability. The Magic Knights reluctantly accept Clef's words as truth and embark on a journey to save Cephiro from the clutches of evil.