Ancient ruins are found at Shinanome High School in Japan. Makoto Mizuhara, a young student, who has recently been confronted by school president, Katsuhiko Jinnai, for finding out things that Jinnai would rather keep secret, unlocks the secrets of these ancient ruins. After unlocking the ruins, a young girl appears and whisks Makoto, Jinnai, Nanami Jinnai, the younger, spunky sister of Jinnai, and Mr. Fujisawa, the drunk history teacher, to El-Hazard: The Magnificent World.

Following Ifurita's selfless sacrifice to save El-Hazard from the out-of-control Eye of God, Makoto Mizuhara is left with a profound sense of loss and a new, desperate mission: to somehow reunite with her across time and space.