A mysterious nightmare disturbs Fuyuki Hinata, where he witnesses the Keroro squad being turned to stone and the world facing an unknown destruction. Upon waking, he receives a strange stone statue from their friend Alisa Southerncross, a relic taken from Easter Island that bears an uncanny resemblance to the alien Sergeant Keroro himself. Intrigued, Fuyuki convinces Keroro to embark on a secret adventure to the real-world island famous for its Moai statues, hoping to uncover the connection.

As their aircraft approaches the South Pacific island, the pair is shot down by a sudden, violent attack from an unseen enemy, separating them in the process. Lost and alone, Fuyuki discovers that the island is a nexus of supernatural forces. He encounters the Mana, playful, colorful spirits that inhabit the land, and a mysterious pair of twins named Io and Rana. These children possess the extraordinary ability to manipulate souls and time, revealing that the island is also the domain of a legendary and destructive evil spirit.

This malevolent entity, AkuAku, is a powerful, cyclopean purple wraith who seeks to eradicate humanity. His terrifying ability is to absorb the knowledge and skills of others, copying their powers and fusing them with his own form. One by one, he hunts down the members of the Keroro Platoon—Tamama, Giroro, Kururu, and Dororo—absorbing them and transforming into twisted, powerful versions of the soldiers called AkuKeronians to use as his weapons. Even Sergeant Keroro falls, his body seemingly destroyed by the onslaught.

Separated from his friends and facing an unbeatable foe, Keroro's consciousness is transported back through time by the twins' power, transforming his very soul into the original stone statue found by Alisa. This act of temporal magic allows him to tap into an ancient power, awakening not as a simple invader, but as the legendary Maha Maha, the island's mythical guardian deity—an enormous, plant-like entity with a sprout on its head. Now reborn as the ultimate protector, this new Keroro must battle AkuAku to rescue his comrades and prevent the ancient evil from consuming the entire world.