Three teenage girls on a school trip to Tokyo Tower are suddenly enveloped in a blinding light and transported to the fantastical land of Cephiro. Hikaru Shidou, Umi Ryuuzaki, and Fuu Hououji are strangers who quickly learn they have been summoned to become the legendary Magic Knights, the land's only hope for salvation. Cephiro is a world where willpower directly shapes reality, and its peace is maintained by a single individual known as the Pillar, who offers constant prayers for the realm's well-being. The current Pillar, Princess Emeraude, has been captured by her high priest, Zagato, plunging Cephiro into chaos as monsters born from people's fears begin to roam the land.

Guided by the high priest Clef and a strange, pink, creature named Mokona, the three girls must find three legendary mecha known as Rune Gods. Each girl awakens to a specific elemental power: Hikaru, the spirited and determined leader, wields the power of fire; Umi, the wealthy and initially reluctant swordswoman, commands water; and Fuu, the intelligent and calm strategist, controls the wind. Their quest to find the Rune Gods and forge magical weapons takes them across the varied landscapes of Cephiro, where they face Zagato's loyal minions and learn to trust one another. They are aided along the way by allies such as the swordsman Ferio and the blacksmith Presea.

Upon finally confronting Zagato and reaching the imprisoned Princess Emeraude, the Magic Knights discover a devastating truth. Emeraude was not a helpless victim; she had fallen in love with Zagato. Because the Pillar must dedicate all their prayers solely to Cephiro, her love for one man weakened her ability to sustain the world. Unable to kill herself or allow Zagato to be harmed by anyone from Cephiro, she summoned the Magic Knights from another world to be her executioners. Forced to fulfill their tragic duty, the girls slay both Zagato and Emeraude, which saves Cephiro but leaves it without a Pillar. Their mission complete, Hikaru, Umi, and Fuu return to their own world.

The second story arc begins when the three girls are summoned back to Cephiro, which is on the verge of collapse without a Pillar to sustain it. The power vacuum has drawn the attention of three technologically advanced, warring nations from other worlds: Autozam, Fahren, and Chizeta, each seeking to claim the Pillar system for themselves. Joined by new allies, including Lantis, Zagato's younger brother, the Magic Knights must defend the crumbling land while also facing a new threat from the high priestess Debonair.

As they struggle to protect Cephiro from these invading forces, the girls learn that one of them must be chosen to become the new Pillar, a position that demands the complete sacrifice of personal freedom and love. The three rival commanders—Eagle of Autozam, Geo of Fahren, and Aska of Chizeta—each have their own desperate reasons for wanting to control Cephiro. In a final confrontation, Hikaru is chosen as the Pillar but ultimately rejects the system itself. She uses her wish to free Cephiro from relying on a single individual, allowing all its inhabitants to shape their own future through their collective will. Having restored true peace, the Magic Knights finally return home, their bond as friends unbreakable.