One day in the bustling city of Shibuya, a boy named Neku Sakuraba finds himself holding two black pins that enable him to read the minds of people around him. However, these pins also give him the ability to see the "Noise," hostile creatures capable of "erasing" people from existence. After discovering that he is trapped within the confines of the city, Neku receives a message regarding a mission that will nevertheless erase him should he fail.

While trying to fend off a Noise attack, Neku meets a girl named Shiki Misaki who asks him to form a partnership pact with her to fight against the monsters. Shiki explains that she and Neku have become "Players" participating in the "Reaper's Game"—an event spanning over seven days, each featuring a different mission.

As Neku and Shiki both strive to survive each day that passes, they begin to meet other Players and Reapers alike, battle stronger Noise, and learn the truth behind the mystery that this game is shrouded in.