A gigantic monster known as Gaea-tima rises from the sea and devastates the small Japanese seaside town of Sukuba. Ten years after this catastrophe, the resilient community has rebuilt itself into an unlikely tourist destination, capitalizing on the notoriety of the attack. The town’s dark past is now a selling point, with a local survivor named Miyako making a living by selling handcrafted miniature replicas of the creature that once tried to destroy her home. She is haunted by the trauma of that day, but the economic dependence of her neighbors on the monster’s fame leaves her unable to fully escape its shadow.

This uneasy peace is shattered when a new and different kaiju, Hettorga, emerges to threaten the town. In a shocking turn, the original Gaea-tima suddenly reappears, not to attack, but to engage and defeat this new rival before vanishing once more. This event draws the attention of the kaiju biological research agency FUNE and its head, the determined oceanographer Tatsukuni Matsushima. Investigating the incident, the team makes a startling discovery: Gaea-tima seems to have formed a powerful psychological and biological connection with Miyako, treating her as an object of imprinting. This bond pulls Miyako out of her passive existence and into the heart of FUNE’s operations.

As Miyako struggles with her role as a potential bridge between humanity and the "gigantis," the series expands its scope beyond simple monster attacks. The narrative explores the origins of these creatures and the ambiguous nature of their intentions. When a subterranean kaiju attacks, Gaea-tima defends the region, but this does not quell the fears of the military or the public. The story deepens with the introduction of Hibari Esashi, an enigmatic figure who can control a powerful winged kaiju named Tsubagra. Hibari’s complicated past and her manipulation of the creatures for her own agenda force Miyako and Tatsukuni to question whether coexistence is possible, or if violence is the only language shared by humans and kaiju.

Throughout subsequent arcs, Miyako learns to enter Gaea-tima’s dreams, forging a telepathic link that allows her to understand its motivations. Meanwhile, other residents of Sukuba, such as a kindhearted but bullied young boy named Yutaka who unexpectedly bonds with a different kaiju, further blur the line between friend and foe. As the defense forces scramble to contain the escalating situation, Miyako must confront the central question of the series: whether humanity is capable of responding to immense violence with anything other than more violence, or if a deeper, more symbiotic relationship with these forces of nature is possible.