Two beings from the planet Maron, the young Prince Meru and his devoted attendant Maru, drifted to Earth long ago after their invading fleet became lost. They gradually forgot their original mission and settled into a peaceful life in the deep sea, but never abandoned their desire to rebuild their underwater kingdom by finding the strongest and kindest princess in the world.

Their search leads them to Natsumi Hinata, the fierce and capable older sister of the household where Sergeant Keroro, leader of the Keroro Platoon, is stationed. Using a powerful device called the Mer Ball, which can manifest dreams and memories into reality, Meru kidnaps Natsumi and brings her to a magnificent castle in the deep sea, intending to make her his princess. To counter the immense water pressure and rescue their friend, Kururu develops special protective gear and underwater machines, allowing the Keroro Platoon to venture into the ocean depths.

Upon arriving at the underwater kingdom, the platoon discovers that the city and castle are projections of Natsumi's own memories, specifically a shopping mall from her childhood where she once felt lost and lonely. While being treated with great honor in this dream-like world, Natsumi begins to understand Meru's loneliness and the feelings of his loyal attendant, Maru, who secretly harbors deep affection for the prince. As Meru's plan escalates to transforming the entire Earth into a water planet like his lost homeworld, the Keroro Platoon must fight to free Natsumi and stop him. In the end, through Natsumi's empathy and understanding, she helps Maru realize her own worth, and Maru becomes the true princess, returning to space with Prince Meru to rebuild their kingdom together.

The film also features a short companion piece that explores the childhood of the Keroro Platoon, revealing the secret of Kururu's distinctive yellow body.