In this world, divine beings exist beyond mortal comprehension, with no concept of good or evil. These gods threaten peace across Japan through destructive physical manifestations, the manipulation of dreams, and warps in the very fabric of reality, leaving humans completely at their mercy. Agent Katagishi and his junior partner Miyaki belong to a secret government organization tasked with investigating these supernatural incidents, handling cases that involve deities and the dangerous humans who worship them. Throughout their work, Katagishi remains determined to track down his missing wife, even if it forces him to confront a terrible truth.

The story follows this pair as they travel to small towns across Japan investigating phenomena known as Divine Incursions, inexplicable activities that can only be explained if one accepts that the gods of nature and place are as real as the people there. Katagishi is a dour, chainsmoking misery of a man, while Miyaki serves as his cheerful and extroverted partner. Their superior, Mitsuji Rokuhara, is Katagishi's former brother-in-law who runs the Divine Incursions Special Investigations Division.

The narrative unfolds through intersecting but not quite interconnected cases. In one town, massive body parts have fallen from the sky every year since 1997, beginning when a huge right arm filled the school's twenty-five-meter pool during the annual festival. The villagers collect these body parts in an old school building, having moved the protective stones meant to honor the local deity in the name of progress. Katagishi and Miyaki investigate the folklore surrounding the area, learning of a huge god that once stayed on the nearby mountain.

Another case brings them to a town known as the home of The God That Ate Men, where they investigate incidents suggesting someone has truly encountered this deity. A third case takes them to a tourist town by the ocean next to a less popular mountainous village, where a local legend tells of a mermaid saved by a fisherman. When the townspeople cared for her, she eventually invited them to eat her flesh for immortality, but the truth behind this folklore becomes increasingly unsettling as the agents investigate.

Throughout these investigations, the two agents observe and interview villagers, coming to their own conclusions about each situation. The gods in this world are not metaphors but real beings whose actions stem directly from what humans do or fail to do. When worship of a local deity stops or protective stones are moved for development, the gods make themselves known, refusing to be forgotten. Technology and progress may appear to bring prosperity, but often not with the gods blessings. The series explores how folklore manifests in the modern world when people have largely forgotten the original gods and their stories, causing the deities actions to become even more unknowable or altered by changed human behavior and environmental elements.

The first volume is structured with each chapter named after what a god is known for or has become known for, including The God That Descends in Pieces and The Unknown God. Katagishis personal quest to find his missing wife serves as an ongoing thread, with the politics of memory and the intersection of belief and divine existence helping bring the volume to its conclusion. The series is complete in three books, with the second volume serving as a prequel showing how the Divine Incursions Task Force was established, fell apart, and later became the Special Investigations Division. This prequel follows Sadahito Uyu, a conman with the ability to see the supernatural, who is recruited by a former homicide detective and an associate professor of folklore studies.