When seventeen-year-old Makoto Mizuhara (水原 誠 Mizuhara Makoto) went to testify against Student Body President Katsuhiko Jinnai in an impeachment hearing, Jinnai attacks him in an effort to prevent his testimony when time comes to a standstill. Making his way down to some ancient ruins underneath the school, Makoto discovers a mysterious, beautiful woman who sends him and the others still on the school campus to the world of El-Hazard.
Once in El-Hazard, Makoto meets up with his history teacher, Masamichi Fujisawa, and after a brief encounter with some Bugrom soldiers, the two rescue Princess Rune Venus of Roshtaria, who had been traveling to learn news of her missing sister, Fatora. As it turns out, Makoto bears an uncanny resemblance to the missing princess, and he's reluctantly recruited into impersonating Fatora. He goes along with the plan, hoping that doing so will allow him access to the Eye of God, which might have the power to return him to Earth. Over the course of the series, he becomes enthralled with Ifurita, and is oblivious to the advances that Nanami and Shayla-Shayla both make on him.
After Ifurita is catapulted far away into time and space, Makoto vows to uncover the secrets of the Eye of God in order to come rescue her. While Yokohama beach Makoto swallows a pearl and falls in love with Shayla-Shayla causing him to get into a fist fight with Jinnai who had the same thing happen to him.
Makoto's journey from Earth to El-Hazard endowed him with a special ability to activate and link with ancient devices of a lost El-Hazard civilization, including the Eye of God and the Demon God, Ifurita.