Three junior high school students Hikaru Shidou, Umi Ryuuzaki, and Fuu Hououji are pulled from a school trip into a dark and desolate version of Tokyo. The city lies silent and ruined, with the ominous castle of the magical world Cephiro now standing at its center. This is not the Cephiro of legend, but a corrupted realm spilling into Earth's dimension under the influence of the evil high priest Zagato. The girls are identified as the legendary Magic Knights, destined to wield powerful godlike beings known as Mashin to save both worlds from complete destruction. However, the trio is immediately separated. Hikaru is confronted by the ice witch Alcyone but is rescued by a mysterious young man named Lantis, who seals her within a magical maze to test her worth. Meanwhile, Umi and Fuu flee through the empty streets of Tokyo, hunted by Cephiro's warlocks, and must awaken their own Mashin if they hope to survive.

The story unfolds across a condensed yet emotional narrative that reinterprets the original Magic Knight Rayearth saga. Unlike the television series, this alternate retelling places the heroines in a post-apocalyptic version of their own world, forcing them to confront their destinies without the guidance of Princess Emeraude. As Hikaru battles through Lantis’s labyrinth to prove her power, Umi and Fuu struggle with fear and isolation, eventually forming contracts with their own colossal warriors. The plot builds toward a final confrontation against Zagato’s forces, culminating in a tragic revelation about Princess Emeraude, whose unspoken wish and sacrifice lie at the heart of Cephiro’s collapse.

The main characters include the spirited and courageous Hikaru Shidou, the disciplined and refined Umi Ryuuzaki, and the gentle but intelligent Fuu Hououji. Key figures from Cephiro include the conflicted knight Lantis, the vengeful Alcyone, and the mysterious creator being Mokona. This special edition, re-edited by chief director Toshihiro Hirano, compresses the three-episode OVA series released in 1997 into a single seventy-five minute film. It features approximately five minutes of new animated cuts and re-recorded dialogue to accommodate the restructured story, with a notable narrative focus on the character Eagle, revealing his hidden true intentions.