Makoto Mizuhara, a high school science prodigy, is busy readying his latest invention for the school festival with his best friend Nanami Jinnai at his side. Nanami's brother, the scheming student council president Katsuhiko Jinnai, is under fire for botching the festival arrangements and suspects Makoto is scheming to take over his role. One evening, while Makoto, Nanami, and their teacher Masamichi Fujisawa are taking a rest, Jinnai slips into the science lab and tampers with Makoto's device. This triggers a sudden portal that hurls all four of them into a different world!
Upon arriving, Makoto finds himself under attack by a swarm of enormous insect-like monsters. Fleeing, he runs into Fujisawa and a young woman named Rune Venus. After Fujisawa drives the monsters off, a procession of officials shows up, searching for Rune—their princess. They explain to Makoto and Fujisawa that this realm is called El-Hazard and escort them to the palace of the kingdom of Roshtaria. Although her advisers are wary of the strangers, Rune declares them guests and quickly becomes friendly with Makoto. Not knowing that Nanami and Jinnai are also in this world, Makoto sets out to find a way back to Earth.