Sergeant Keroro and his four subordinates came from the planet Keron to the Earth to conquer. However, without notice, they began to enjoy the life on the Earth. Keroro was supposed to stay with Hitana to get the chance to conquer the Earth, but he became friend with Hinata's son, Fuyuki. Today, as usual, Keroro goes to buy his favorite Gundam plastic model with Fuyuki. On their way home, they find a small shrine, and enter. There, they find a vase, and happens to break it. Since the next day, strange things happen all over the town and people are in panic. Inside the vase, Kiruru, Keron's ancient ultimate weapon was sealed. At the moment, Mirara who holds the secret of the Kiruru appears and informs them of the only method to save the Earth. However...

Another Kiruru appears in the South Pacific, but it was defeated by two unknown entities that look like Keronians, with subtle differences. Meanwhile, Keroro and the gang goes for a trip sponsored by Momoka to a private island. There, an alien named Meru, who claims himself as the prince of the deep sea, captures them, and aims to make Natsumi his princess, and that they had captured Keroro, who pleads to them to assist the Keroro Platoon, only to be kicked out.

The movie begins with Fuyuki Hinata and the Keroro Platoon exploring an abandoned temple in the mountaintop city of Machu Picchu in Peru. While on the exploration, Keroro accidentally sets off a trap, and by chance they find a hidden chamber with a large blue crystal in the center, on a stand that has a key in it. Keroro leans on the key, causing the room to activate a mysterious machine, this caused the entire temple to shake. As soon as the group realized what was happening, they run out of the room. While running, Keroro accidentally loses his Kero Ball while Fuyuki catches a fleeting glimpse of a glowing young woman as he is running out, and tells Keroro that there was a girl in the room, but he is forced to leave the room before he can say anything else. The group successfully escapes, while the girl (now sprouting a pair of glowing wings) watches them leave - while back in the chamber, something is growing within the crystal...

Mysterious giant beings called "Ryū no Shippo" (Dragon Tails) appeared across the world. Due to the danger it could bring, the Keroro Platoon did a worldwide research on the Dragon Tails, but Tamama suddenly disappeared during the research. Because of this, the whole platoon started their search for Tamama and ended up in Mont-Saint-Michel, France where they met mysterious girl named Sion, who holds the mysterious Ryū no Hon (Dragon Book). But little they know about the secrets about her and the worldwide calamity that would destroy the entire world, as they know it...

Seeking to unlock the mystery of a strange stone statue that looks exactly like their Sergeant, the members of the Keroro Platoon find themselves engaged in a great adventure.