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.

Magic Knight Rayearth II was released on DVD by Media Blasters in seven volumes on March 25, 2003. The series was later remastered and released on Blu-ray and DVD by Discotek Media on January 31, 2017 and February 28, 2017 respectively.