Little time has passed since the Magic Knights’ final confrontation with Princess Emeraude’s "Mashin." Still haunted by the princess’ death, Hikaru Shidou returns to Tokyo Tower. There, she meets her friends Umi Ryuuzaki and Fuu Hououji for the first time since their spontaneous quest to save Cephiro. Plagued by nightmares of the realm she had left behind, Hikaru is relieved to find that her companions too want to return and serve the kingdom they once so dutifully protected. The Magic Knights’ wish is answered, for at the top of Tokyo Tower, the three are blinded by the same great light they had seen on the day they first met. Once more on the back of a flying fish, the group returns to Cephiro—a world now desolate and in ruins. With the collapse of the Pillar's power, monsters freely roam the land while three nations seek to annex Cephiro with hopes of seizing the Pillar for themselves. Complicating things further is the mysterious Lady Debonair, who proclaims herself to be the rightful heir of the fallen country. Now confronting graver stakes and radically different enemies, the three Magic Knights set forth once more to save Cephiro and bring peace. With the bonds they have forged together, the trio stands united in the face of such a great challenge. 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.