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.

After Alielle and Makoto have their "interesting" first meeting, Alielle explains how she went off to see her parents while the princess was kidnapped. Eager to help Makoto and Fujisawa on their journey to see the Priestesses of Mount Muldoon, Makoto is given Ura, Fatora's pet cat who also doubles up for armour.

Makoto Mizuhara, Nanami, and Mr. Fujisawa find themselves on an unexpected detour. Their journey through this new world leads them to a traditional hot spring resort. Makota must maintain his disguise as Princess Fatora in an all-woman spring.

Hearing the news that Jinnai is after the legendary demon god, the priestesses, accompanied by Makoto, Alielle, Fujisawa and Nanami, set out to travel to the Forbidden Island, the holding place of the demon. However, when they arrive, they discover that Jinnai has been tailing them since they left and the whole thing was a giant ploy to show the Bugrom the way to the island.

As the battle for El-Hazard intensifies, Makoto Mizuhara and his allies, including the Priestesses of Muldoon, find themselves on a quest to confront a powerful force. Meanwhile, Katsuhiko Jinnai, now leading the Bugrom forces, sets his sights on unleashing the legendary Demon God Ifurita, a being of immense destructive power.

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.