While on a school field trip to Tokyo Tower, three young girls—Hikaru, Umi, and Fuu—are suddenly whisked away to the magical realm of Cephiro. There, they are met by Master Mage Clef, who informs them that they have been called forth to serve as the legendary Magic Knights and rescue Cephiro from peril. The girls are far from thrilled by this revelation and simply wish to return home. Clef goes on to explain that they must locate the three Rune Gods to aid them in battle, and he grants each of them armor and magical abilities. They then learn from Clef that High Priest Zagato has abducted Princess Emeraude, the Pillar of Cephiro. It is the Pillar's sole duty to sustain Cephiro's life and harmony through her prayers; without Princess Emeraude, Cephiro would inevitably descend into chaos. To ever have a chance of going back home, Hikaru, Umi, and Fuu must confront Zagato's minions and find the Rune Gods. In the process, they come to understand that friendship and loyalty are the only things they can trust in the deteriorating world of Cephiro.