Sergeant Keroro is the Captain of the Space Invasion Forces Special Advance Team of the 58th Planet of the Gamma Storm Cloud System, sent to the planet Pekopon (aka Earth) to collect intelligence for his planet's invasion force. He is also a frog. After his ship crash-lands in the planet, he takes shelter in the Hinata household, but the two kids, Fuyuki and Natsumi, find him and take away his alien weapons. When his people discover that the Pokoponians are aware of him, Keroro is abandoned - left to fend for himself in this hostile world. But he's not alone - four other pre-invasion agents were are also lurking on Earth. It's invasion of the weird in this wacky comedy hit!
In a freak lightening accident, the violent aggressive Momoka is spun out of the usually sweet and docile one. The spiked hair Momoka using the vulgar male pronoun "ore" takes over the base and forms the new "Momoka Platoon" and starts the invasion of earth. Defeated, the inept Keroro goes into hibernation. Just as the violent Momoka is ready to push the button to launch the missile, the docile Momoka arrives in time to stop her other self from destroying Earth. They agrees to join back together in one body and will one day declare their love for Fuyuki. Keroro, revived, offers to join them through synchronized swimming. After a wonderful performance, a complete Momoka emerges from the pool. However, another complete form also emerges—the Keroro-Giroro combination.
Members of the platoon and their human allies witness Mois beating up people and taking their money. In disbelief, they try to find clues to Mois's secret activities, but not even her videogram to her father yields any. Hurt that no one believes her innocent and at the same time embarrassed to tell them of her activities, Mois runs out. In pursuit, they encounter a delinquent Mois getting ready to harm some of Natsumi's classmates. To the rescue, Natsumi fights Mois, until another Mois appears. Through a flashback, Mois reveals that she modelled herself after Asami, a brave girl who had once defended the weak. Now Asami has become a delinquent and they must intervene to bring her back from her lone wolf days. Through Kururu's invention which generates holograms, Fuyuki's script, Mois's acting, and everyone else's assistance, they manage to have her return home.
It's summer, and the school swimming pool is open for use. While Fuyuki has been dreading this all year (he can't swim), Keroro hatches a new scheme to infiltrate the swimming pool and have some fun on his own, resulting in a confrontation with Natsumi in the pool, where Keroro's amphibious advantage over her is exploited to the fullest. After the historic Earth versus Keron Swimming Meet, a second interplanetary competition begins at nighttime, as humans and Keronians duel each other with the scariest ghost stories they can think of. While Fuyuki's little-known talent for ghost stories wins the day, the only real loser here is Giroro, who gets jerry-rigged to a meter and subjected to all the scares (and some physical violence) from both sides.
It's time for another important summer ritual, the family trip to Doinaka Beach, but Hinata Aki is uable to accompany the children due to work commitments, leaving Natsumi and Fuyuki without an adult guardian, until Kururu reveals his latest invention, an age manipulation beam that turns Natsumi into a full-grown adult. An unexpected side effect causes Natsumi to utter 'old-man' jokes involuntarily, while Keroro's hidden angle and true reason for infiltrating the beach is revealed—the super-rare 'Dangale' knockoff model kits, offered as a prize for entering the Swimsuit Beauty Stand-Up Comic Competition.
Low on invasion funds, the platoon takes on food vending and gaming jobs at a festival. Keroro's unscrupulous manners are challenged by Natsumi and they face off at a turtle fishing game. Defeated, the frogs are ready to leave the festival, until Natsumi told them that as long as they are legitimate, it doesn't matter who attends the festival. Stirred by her compassion, Giroro dashes to stop Keroro trump card, but instead find himself, Keroro, and Tamama sent into the air as part of the night's fireworks. The red and green are exceptionally beautiful, but no one can see the dark blue color of Tamama. Witnessing the power of radio, the platoon, minus Dororo, set out to jack all the stations and put on their own programming. Different and novel at first, the radio progam gains a huge draw. However, a poorly impersonated Sumomo-chan by Giroro quickly reverses that and soon listeners turn off their radio one by one.
The trip to the beach that Aki promised the children in episode 18 gets put off again due to car trouble, but living with aliens proves to have its advantges, as Natsumi finds out about the Keroro Platoon's high-tech submarine, and begs them to take her to the beach, putting a slight dent in Keroro's newest scheme, to conquer the world through its oceans. Fuyuki comes along, hoping to gather some oceanic research to complete a school project, but winds up meeting a mysterious girl. The girl's true origins are hinted at as the Keroro Platoon's undersea flag-planting activities are met with substantial opposition—the ancient Nontolma civilisation, already angered by humanity's pollution of its oceans, and looking to make an example to the Keroro Platoon.
Keroro engineers some falsified invasion footage to send to Keron high command (and make some quick cash on the side) but a sudden city-wide power outage leaves this newest scheme in ruins, as Kururu conveniently forgot to save his progress. Also feeling the heat (literally) is Natsumi, without air-conditioning to beat the rising summer temperatures. Koyuki leaps to the rescue with some traditional summer rituals of her own, while Keroro's backup plan for the next power outage is less than successful. Aki's car trouble has passed, resulting in a brief glimpse at her unique driving skills as the Hinata family (and three Keronians stowing away in the boot) take another field trip, to the countryside this time. Giroro runs off to do some survival training in the forest; Keroro joins Fuyuki for a round of baseball, but gets chased into the forest by a huge dog; Tamama engages a seemingly normal rhinoceros beetle in a martial arts duel; and we meet Grandmother Hinata, who not only learns about the Keronians on her own, but secretly lends them a hand.
Just as a complacent Keroro is happy being unchallenged in his position as the leader, a flying arrow message is shot from HQ: "Tamama is captain." Keroro and the others are speechless at first, but following orders, Tamama becomes captain. Power corrupts Tamama and he soon turns into a monstrous tyrant by banishing anyone who disagrees with him, even his most beloved Gunsou-san. What will now happen to Keroro?
Keroro steals the Kero Ball from Fuyuki's room, and accidentally clones hundreds of himself, all just as lazy as the original. Kururu's attempt to rectify this situation turns them into mindless drones under Keroro's control, but just as this new power starts corrupting him, Kururu discovers that the malfunctioning Kero Ball may pose a bigger threat to Keroro himself.
The show shifts its focus back to Japanese culture this week, as we witness the autumn School Sports Meet - yet another thing Fuyuki has been dreading all year (see episode 17). Natsumi on the other hand is excited about running in the three-legged race with her mother Aki - until she learns that work commitments have held up Aki yet again. Keroro schemes to win Natsumi's gratitude by infiltraiting the sports meet with Giroro and stalling the events until Aki can make it, while Tamama and Dororo head to Aki's office and attempt to speed up her work - but both efforts seem doomed to failure, forcing Giroro to act on his own.