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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?

Soon after Hikaru, Umi, and Fuu return to Tokyo, the three of them meet at Tokyo Tower to talk. Hikaru says that she wishes they could return to Cephiro and do something good for the land that Princess Emeraude protected so dearly. Umi and Fuu agree. Suddenly, a light appears in the sky and they are transported to Cephiro. Clef explains to them that with no Pillar to keep Cephiro peaceful, it has fallen into chaos. Monsters are multiplying and the land is becoming desolate. All the remaining inhabitants of Cephiro have moved into a magical castle. Clef also tells the girls some alarming news; three other countries, Chizeta, Fahren, and Autozam are trying to invade Cephiro and take over the Pillar system for their own purposes. The girls must stop the invaders as well as the mysterious and evil Lady Debonair, who believes she is the rightful Pillar, all the while desperately hoping and searching for a new Pillar to make Cephiro into the beautiful land it once was. (Source: ANN)

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. [Written by MAL Rewrite]