On an ordinary day, high school student Saneatsu Narita receives a cryptic message on his computer posing a simple yes or no question. The following morning, he awakens to find Tokyo deserted. He discovers that nearly everyone who did not see that message has died. The few survivors, including Saneatsu's best friend Ryūta Ichinose and student council member Saaya Fujishiro, are soon contacted by a being calling himself the Emperor. The Emperor announces that they are all participants in a deadly game called Tasuketsu, or Absent Majority. Each day, the Emperor presents a binary question. The rule is brutal: those who answer with the majority will die. This premise forces the remaining population of Tokyo into a life-or-death struggle where consensus is a death sentence.

The protagonists are a small group of students from the same high school, including the determined Saneatsu, his loyal friend Ryūta, the level-headed Saaya, and others such as the sardonic Kazuhiko Satō, known as Ippiko. As the game progresses, they discover that each player possesses a unique Privilege, a special ability that can only be used once. These powers, ranging from altering votes to gaining information, become crucial strategic tools. The survivors must navigate a desolate urban landscape, racing against a daily clock while trying to deduce the intentions behind the Emperor's seemingly random questions. The group faces a constant ethical dilemma: cooperating could lead to mass death if their shared answer becomes the majority, while betrayal might ensure individual survival.

The manga is structured into multiple parts, beginning with the initial chaos of the game's announcement. As the story develops, the survivors encounter other factions with different philosophies on how to beat the game. A notable narrative shift occurs when the survivors realize the Emperor is not a distant, faceless entity but is operating from a location within the city. This leads to a direct confrontation where Saneatsu and his allies attempt to storm the Emperor's stronghold. In the final arc, the true nature of the game is revealed as a massive social experiment designed by the Emperor to observe human behavior under extreme duress. The conflict culminates in a final vote where Saneatsu uses his intellect and Privilege to outmaneuver the Emperor, ending the game. However, the resolution leaves lingering questions about the long-term psychological impact on the survivors and the implications of the experiment's conclusion.