In the story, Makoto Mizuhara, a brilliant high school science student, is preparing his newest invention for the school festival, alongside his close friend Nanami Jinnai. Nanami’s brother, the cunning student council president Katsuhiko Jinnai, feels threatened by Makoto and believes he is plotting to oust him from his position. One night, while Makoto, Nanami, and their teacher Masamichi Fujisawa are taking a break, Katsuhiko sneaks into the lab and interferes with Makoto's equipment, inadvertently activating a portal that transports all four of them to another world.
Upon arrival in this new realm, Makoto is immediately confronted by a horde of giant, insect-like creatures. As he flees, he encounters Fujisawa and a young woman named Rune Venus. With Fujisawa's help, they manage to fend off the attackers. Soon, a group of officials arrives, seeking Rune, who is revealed to be the princess. They inform Makoto and Fujisawa that they are in El-Hazard, the kingdom of Roshtaria. Despite initial skepticism from the royal advisors, Rune welcomes the newcomers and quickly forms a bond with Makoto. Unaware that Nanami and Katsuhiko are also stranded in El-Hazard, Makoto embarks on a quest to discover a way back to Earth.