It is the year 2004 AD, and pandemonium breaks as a mysterious frog-like alien race fills the sky with UFOs—or so 12-year-old Fuyuki Hinata dreams. Coincidentally, Sergeant Keroro, leader of a preliminary squad for the Keronian invasion of Pekopon—the alien name for Earth—begins his mission by invading Fuyuki's home. After subduing the boy and his sister, Keroro plans to reunite with his comrades and return to the mothership to repair his invaluable invasion device, the Kero Ball. Unfortunately, he receives word that headquarters has abandoned his unit's retrieval due to an unprecedented issue that forced the rest of the Keronians to flee.

Consequently, Keroro is forced to stay at the Hinata residence together with the friendly, starry-eyed Fuyuki; his athletic, short-tempered sister Natsumi; and their hardworking, attractive mother Aki. Now stuck until further notice, Keroro and his platoon spend each day plotting world domination, but are thwarted each and every time by various unexpected factors. Nevertheless, as they live alongside humans, they learn to treat them as friends and allies, forming comedic yet meaningful connections that make their lives on Earth worthwhile.