The signing of a peace treaty has secured a tenuous ceasefire between mankind and the Zex, beings who emerged from space/time rifts connected to mysterious, distant worlds. Partnered with a Zex named Rigel, Azumi Kakamigahara must shoulder the fate of her own idyllic world. The unlikely pair head to newly established Fujimisaki Academy, where their destinies await.

High school science-whiz Makoto Mizuhara is working on his newest project in preparation for the school festival, alongside his best friend Nanami Jinnai. Nanami's brother and Makoto's lifelong rival, the unscrupulous student council president Katsuhiko Jinnai, is under scrutiny for mishandling the school festival planning and is convinced that Makoto is plotting to steal his position. One night, as Makoto and Nanami are taking a break with their teacher Masamichi Fujisawa, Jinnai sneaks into the science lab and sabotages Makoto's device, which suddenly opens a portal that flings all four of them into another world! Upon arrival, Makoto is immediately attacked by a horde of giant bug monsters. While running from them, he comes across Fujisawa and a girl named Rune Venus. After Fujisawa fights off the monsters, a group of dignitaries arrives, looking for Rune, their princess. They inform Makoto and Fujisawa that they are in a world called El-Hazard and take them back to the palace of Roshtaria, their kingdom. Though her advisors are suspicious of the newcomers, Rune decrees that they are to be treated as guests and quickly befriends Makoto. Unaware that Nanami and Jinnai are in this world as well, Makoto gets to work trying to figure out a way back to Earth.

Nobita had to find a topic for his summer break research homework. As he was blaming everything to Adam and Eve for sinning and causing their descendants to suffer (from homework), Doraemon decided to provide him with a gadget to observe the creation of the world so that he may write it in a diary-like report. Suneo, Giant and Shizuka eventually joined them and together they watch over the birth of tribes and civilizations. Meanwhile, the time patrol is looking for an illegal time machine whose controllers accidentally heard Giant speaking of the genesis diary project. They captured Giant and Suneo; leaving Nobita, Shizuka and Doraemon to watch over the genesis set and to rescue them. (Source: ANN)