The story unfolds in a contemporary Japanese high school, where the mundane lives of students are shattered when a beautiful, ethereal goddess appears before them. She declares that the world is about to end and that she has descended to select a single human to become her partner, who will rule over the new world alongside her. However, she does not choose based on virtue or strength. Instead, she forces the entire student body to participate in a series of cruel, arbitrary, and often absurd games. The first of these is a sadistic test of courage and obedience: everyone must draw a card that determines whether they live or die, with the goddess deriving entertainment from their terror.

The central protagonist is a cynical and withdrawn boy named Hiroshi, who initially believes this is an elaborate prank. His detachment quickly crumbles as students around him are violently erased for failing the goddess's whims. He is joined by a small group of survivors, including his childhood friend who harbors a fierce will to live, and a quiet, enigmatic girl who seems to understand the goddess's nature more than she lets on. As they navigate each new deadly trial, they realize that the goddess is not a single entity; she is one of many divine beings, and their school is merely one arena in a global competition. The true conflict arises not just from surviving her games, but from understanding that the goddess is a lonely, capricious force seeking a human who can challenge her nihilistic worldview.

The setting is initially confined to the claustrophobic halls of the school, which becomes a labyrinthine death trap where classrooms transform into puzzle rooms, hallways shift, and the rules of reality bend to the goddess's mood. As the narrative progresses, the scope expands to include other students who have formed factions, some seeking to appease the goddess and others plotting rebellion. A major narrative arc follows their attempt to discover the goddess's true name and origin, believing that this knowledge will give them power over her. This arc leads them to uncover that the goddess was once a human girl who died in despair, and her ascension to divinity was a fluke, leaving her trapped between the mortal and divine realms, acting out her unresolved traumas through these deadly games.

A second significant arc deals with the aftermath of a failed rebellion, where the goddess splits the remaining survivors into two groups: one to be tormented with visions of their worst memories, and another to be granted temporary "gifts" of power to hunt the first group. This forces Hiroshi to confront his own repressed guilt and selfishness, realizing that his survival instinct has cost the lives of others. The climax of this arc sees him willingly sacrifice his chance to win the competition to protect a fellow student, an act of genuine selflessness that stuns the goddess and fractures her cold demeanor. This moment shifts the narrative from a simple survival horror into a psychological exploration of despair, hope, and the meaning of human connection in the face of an indifferent or hostile cosmos. The manga concludes with Hiroshi and the goddess reaching an ambiguous standoff, where he refuses to become her partner or her toy, forcing her to confront the possibility that her games have created a human she cannot control, leading to a final, open-ended confrontation about the fate of both their worlds.