The story begins when Fuyuki Hinata and the Keroro Platoon travel to the ancient mountaintop city of Machu Picchu in Peru to explore its ruins. During their expedition, the hapless Sergeant Keroro accidentally triggers a hidden trap, leading the group into a secret chamber. In the center of the room stands a large blue crystal on a pedestal with a key inserted into it. When Keroro leans against the key, it activates a mysterious machine, causing the entire temple to shake violently.

As the group flees from the collapsing structure, Fuyuki catches a brief glimpse of a glowing, mysterious girl with wings standing motionless in the chamber. He is forced to escape before he can investigate further, and the group returns to Tokyo, with Fuyuki unable to forget the enigmatic figure.

Back in the city, a new and terrifying threat emerges without warning. A powerful alien warrior appears, one who is the spitting image of Keroro but with a far more ruthless and competent demeanor. This Dark Keroro arrives with his own elite squad of lieutenants, including a Sun Wukong-inspired fighter and a former commanding officer of Giroro. Unlike the lazy Keroro Platoon, Dark Keroro is a superior replica who swiftly begins a full-scale, efficient invasion of Earth using advanced technology and mind control. The Keroro Platoon must now put aside their usual schemes and domestic squabbles to face their most personal challenge yet: a fight against their own dark mirror. The fate of the planet depends on whether the original Keroro can stop his superior duplicate, while the mystery of the girl in the crystal proves to be deeply connected to the conflict.