On a field trip to Tokyo Tower, three schoolgirls from different schools — Hikaru, Umi, and Fuu — are pulled into the collapsing world of Cephiro. The mage Clef tells them they have been summoned as the legendary Magic Knights and must rescue the captive Pillar, Princess Emeraude, whose prayers alone keep Cephiro from ruin. To stand against High Priest Zagato and earn a way home, the three must awaken their elemental magic and find the giant Rune Gods.