In the future, the moon is a habitable place with an atmosphere and gravity, hosting a famous tourist attraction. There are also rumors about log earred, rabbit like creatures on the moon who can use magic. Haruka Daichi heads off to the moon during a summer holiday alone because he wants to see the long earred creatures himself. However, he get himself dragged into an millenia-old conflict between two ancient moon races: the long ears race and the Jado race. The Jado race wants to conquer the universe and resurrect certain evil powers to seize control of the Earth. Now the long ears race and Daichi must seek three warriors who can use magic in order to release the Mado King and the long ears race's kingdom, Rabiluna, from the Jado's control. (Source: AniDB, edited)

Little time has passed since the Magic Knights’ final confrontation with Princess Emeraude’s Mashin. Still haunted by the princess’ death, Hikaru Shidou returns to Tokyo Tower. There, she meets her friends Umi Ryuuzaki and Fuu Hououji for the first time since their spontaneous quest to save Cephiro. Plagued by nightmares of the realm she had left behind, Hikaru is relieved to find that her companions too want to return and serve the kingdom they once so dutifully protected. The Magic Knights’ wish is answered, for at the top of Tokyo Tower, the three are blinded by the same great light they had seen on the day they first met. Once more on the back of a flying fish, the group returns to Cephiro—a world now desolate and in ruins. With the collapse of the Pillar's power, monsters freely roam the land while three nations seek to annex Cephiro with hopes of seizing the Pillar for themselves. Complicating things further is the mysterious Lady Debonair, who proclaims herself to be the rightful heir of the fallen country. Now confronting graver stakes and radically different enemies, the three Magic Knights set forth once more to save Cephiro and bring peace. With the bonds they have forged together, the trio stands united in the face of such a great challenge.

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)

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.