Princess Emeraude, who has been maintaining the peace and unity of Cefiro through her strong prayer and inner strength, is captured by the priest, Zagato, her most trusted Guardian. With the last of her powers, Princess Emeraude summons the three girls to Cefiro in hopes of saving it from destruction.

Cefiro is a magical world which materializes from the will power of its inhabitants. When Princess Emeraude prays for Cefiro to be a place of peace and tranquility, it is her will power which transforms Cefiro into a serene paradise. But when she is taken away and held captive, the inhabitants of Cefiro become worried and afraid. It is this fear which creates and unleashes evil forces upon this once idyllic Garden of Eden.

In Cefiro, Doshi Clef waits for the three girls, Hikaru, Umi, and Fuu. On arrival, he tells them why they have been summoned to Cefiro, and they can not return home until their mission is completed. Their mission, as the Legendary Magic Knights, is to awaken the Machine Gods and restore Cefiro to its former glory. Doshi Clef gives each of the girls special magical powers. But before he can explain how to use these powers, they are attacked by Zagato's high priestess, Alcyone. Before sending them off on their mission, Doshi Clef tells them that only by using their inner strength will be able to protect themselves against the evil forces that threaten Cefiro.

Uncertain as to what lies ahead, the three girls boldly carry on with their mission. Each episode shows the girls growing up as they meet and overcome each new challege. With each victory, their armour and magical powers gain strength, preparing them to fight the greatest enemy of all, Zagato.