On a walk home, Keroro and Fuyuki stumble upon a hidden shrine. Upon exploring it, they end up causing damage to a shining orb within it. That night, Keroro finds a big X on his face, which causes him considerable distraught. The next morning, a breaking news story shows that the X has spread to more than just Keroro, giving the people of Tokyo telepathic abilities, including the Hinata Household and the Keroro Platoon. The Earthlings seem to think this is a great gift, but the mark may actually be part of a Pekopon invasion older than time itself.
During a vacation Natsumi is visited by two male and female aliens named Meru and Maru. After becoming the Deep Sea Princess, Natsumi gains feelings for Meru who is haunted by his traumatic past. Having grown accustomed to Natsumi's title, the Keroro Platoon expect a calm vacation. However their vacation is cut short and turns into a fight for survival as an alien creature Fuyuki adops reveals itself to be the enemy of the kingdom and now sends creatures of mass destruction to assassinate Natsumi, and who stands in their way.
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