Sergeant Keroro is a frog-like alien from the planet Keron sent to invade planet Earth (or Pekopon, as his race calls it). He is instead kept as a pet and forced to do chores for the Hinata family, which consists of paranormal maniac Fuyuki, his ill-tempered older sister Natsumi, and their manga-editing mother Aki. Keroro is given his own room in the basement of the Hinata family house, which he refurnishes and uses as a base, not realizing that the room is haunted by a ghost.
In a prequel to the first segment, the Hinata family first discovers and captures Sgt. Keroro while he is scouting inside their house. Fuyuki takes the Keroball (Keroro's weapon) and fiddles around with it, accidentally sending a signal to the Keronian invasion fleet alerting them of Keroro's capture. The fleet abandons Keroro instead of rescuing him, leaving him to perform chores around the Hinata family household.