In a near-future Japan, the colossal kaiju known as Tokyo devastated the capital after emerging from Tokyo Bay on September 2 of an unspecified year. The creature, measuring roughly 210 meters in length and weighing an estimated 85,000 tons, was driven off by the Self-Defense Forces but vanished into Suruga Bay and was presumed lost. Eleven years later, as the frequency of kaiju carcasses washing ashore increases, Tokyo's corpse is discovered stranded on the small island of Ōdoshima in the Seto Inland Sea.

The story follows Akira Honda, a 23-year-old female monster scholar who is summoned by her mentor, Dr. Shinji Serizawa, to join the autopsy investigation of Tokyo's remains. As she reviews the initial survey data, Akira becomes unsettled by the thought that the creature may not actually be dead despite its apparent inactivity. The dissection site is fraught with hazards: parasites infest the corpse, and secondary monsters spontaneously generate from the decaying tissue for reasons that remain unclear. By law, all kaiju-related work must be conducted under the supervision of the Special Mechanized Mobile Unit, meaning the research team operates alongside military operatives and disposal crews. The work site is overwhelmingly male, and Akira faces prejudice and harassment as a woman in this environment.

Akira herself is a survivor of Tokyo's original attack, and she carries deep trauma associated with both kaiju and earthquakes. Nevertheless, she is driven by the conviction that transforming the unknown into known knowledge is the key to disaster prevention, and she is determined to collect as many samples from Tokyo as possible. Clashing with her from the outset is Shūsuke Higuchi, a 32-year-old special operative of the unit assigned to accompany and support her investigation. Higuchi formerly served in a disaster rescue team and witnessed the devastation Tokyo caused firsthand, leaving him with a profound sense of helplessness. He initially insists that Tokyo must be destroyed and disposed of immediately to prevent another catastrophe, viewing the researchers' desire to preserve the specimen as reckless. Over the course of their work together, however, the two begin to understand each other: Higuchi comes to respect Akira's scientific approach, while Akira grows to trust the man who repeatedly puts himself in harm's way to protect her.

The narrative weaves together multiple strands beyond the core autopsy. The disposal operation draws skilled construction and civil-engineering workers from across the country, and the story touches on energy policy, environmental contamination, and the reputational damage suffered by disaster-stricken regions due to kaiju pollution. In the second volume, Akira misses the ferry back to the mainland and is offered a ride by a fishmonger named Amemiya, who claims he can hear the sounds made by kaiju and piques her curiosity. Through these encounters, Akira advances her research, confronts the limits of what science can explain, and works to turn the terrifying unknown into actionable knowledge that might protect against future disasters. Gradually, her struggle becomes not only a scientific mission but also a personal journey to reconcile her trauma and find a path forward in a world that must live alongside monsters.