From the Gamma Nebula's 58th planet, Keron, an elite invasion force is dispatched to prepare for the conquest of a planet they call Pekopon, known to its inhabitants as Earth. The leader of this reconnaissance platoon is Sergeant Keroro, a two-foot-tall, frog-like alien who, along with his squad, is tasked with infiltrating human society and laying the groundwork for a full-scale invasion. However, their mission goes awry almost immediately. Before he can even begin his operation, Keroro is discovered and captured by two siblings, the gentle and paranormal-obsessed middle schooler Fuyuki Hinata and his athletic, hot-tempered sister Natsumi. The platoon's most powerful weapon, the Kero Ball, is confiscated by Fuyuki, and the Keron army, deeming the mission compromised, abandons their advance force and retreats from Earth.

Stranded and powerless, Keroro is forced to take up residence in the Hinata household. He is treated as a cross between a servant and a pet, tasked with chores while living in a small room built into the family's closet. Despite his continued proclamations of interplanetary conquest, Keroro quickly becomes enamored with Earth's culture, developing obsessions with building Gundam model kits, browsing the internet, and eating curry, which consistently derails his invasion plans. Over time, the other members of his scattered platoon reunite and establish their own bases near the Hinata home. These include the sweet-natured yet jealousy-prone Private Tamama, who resides with the wealthy heiress Momoka Nishizawa; the hot-blooded weapons expert Corporal Giroro, who sets up a tent in the backyard and develops an unrequited crush on Natsumi; the eccentric and sadistic communications officer Sergeant Major Kururu, a genius inventor; and the former assassin turned gentle ninja Lance Corporal Dororo, who has sworn to protect the Earth he has come to love.

The narrative follows the daily comedic schemes of the Keroro Platoon as they attempt to fulfill their mission. Their plans, often involving Kururu's bizarre inventions or absurd psychological tactics, are consistently thwarted by the Hinata family and their expanding circle of friends. This includes the arrival of the cheerful and devastatingly powerful planet destroyer, Angol Mois, who becomes a loyal and helpful member of the household. Throughout the series, several notable arcs provide structure to the long-running show. The platoon faces a serious threat from the elite Garuru Platoon, a more competent group of Keronian soldiers who arrive to evaluate and take over the failed mission. Another significant storyline involves a sudden 26-week deadline imposed on the Keroro Platoon to complete the invasion or face the consequences, adding a sense of urgency to their usually relaxed efforts. The series also features arcs where the team confronts the mysterious Syurara Corporation, a rival alien entity, and explores the gang's origins through flashbacks to their mischievous childhoods on their home planet. Through these adventures, the aliens and humans develop an unlikely found family dynamic, turning a mission of conquest into a long-running, chaotic, and heartfelt cohabitation.