Three decades after the great war between the humans and the Zentradi, the U.N. government is developing new technologies to use in their transforming fighter aircraft by running tests on the colony planet Eden. Military test pilots and former childhood friends, loose cannon Isamu Alva Dyson and the Zentradi mixed race Guld Goa Bowman, are selected to each pilot a new aircraft (Shinsei Industries' YF-19 & General Galaxy's YF-21) for Project Super Nova, to choose the newest successor to the VF-11 Thunderbolt variable fighter which is currently still in use by the U.N. Spacy military forces. Their own personal grudges end up disrupting the tests, and begin to wreak havoc on the program.

Senbei Norimaki, known by his nickname Dr. Slump, a genius yet under-respected inventor and roboticist, creates an android by the name of Arale, and poses her as his little sister. What starts as an experiment in robotics turns into an adventure every day for the residents of Penguin Village, a wacky rural community with several colorful characters interacting with Arale and her creator.