The game's story follows Neku over the course of the three weeks that he plays the Game, paired with partners Shiki, Joshua, and Beat for each week, respectively. Neku is confused at first, lacking knowledge of how he died or how he arrived at the UG. As he develops friendships with his partners and starts to understand the rules of the Game, he recalls small details of his death; eventually, he recognizes that he was shot at by Sho Minamimoto, one of the Reapers he faced during the Game. After the first week, only Shiki is allowed to return to the living, and she promises to meet Neku at the statue of Hachiko. However, Shiki has become what Neku values most, and she is used as his entry fee for the second week. At the end of the second week, Joshua seemingly sacrifices himself to save Neku from a bomb created by Minamimoto.Due to Neku and Joshua bending the rules for the game, the game is ruled null and Neku is forced to replay the game a third time. His entry fee this time is all of the other players, meaning Neku cannot form any pacts and stands no chance against the Noise. However, Beat immediately defects from the Reapers and rejoins Neku. Neku and Beat find that the Reapers and the entire population of Shibuya are wearing special red pins that cause them to think the same harmonious thoughts. Without any missions to complete, the two venture to the fabled "Shibuya River", which Joshua was looking for during the second week. At the river, they find Megumi Kitaniji, the Game's Conductor. Kitaniji explains that he created the red pins in an attempt to remake Shibuya, which the Composer challenged him to do; if he fails, Shibuya will be erased.

At that moment, Joshua reappears and reveals himself to be the Composer. Joshua returns the missing part of Neku's memory of death: Joshua himself shot Neku, choosing him to be his proxy in his challenge with Kitaniji. Minamimoto, who had been trying to usurp the position of Composer, was trying to kill Joshua in his weakened state as a human. After failing to defeat Neku by using his friends against him, Joshua gives Neku one last challenge: To fire upon Joshua to determine the fate of Shibuya. Neku is too conflicted to make a choice, and is shot down by Joshua.[18] Neku finds himself once again at the scramble crossing, confused by events.

The game's credits show scenes seven days later. Neku meets Beat, Rhyme, and Shiki (in her real body) by the statue of Hachiko, indicating that Neku and his friends have finally been returned to the RG. Secret reports that can be obtained by completing additional mission