In the second half of the game, Neku starts seeing flashbacks to when he was still alive by reading the mind of his partner Joshua. After several tries, he sees Joshua shoot him and goes the rest of the week believing this, having no choice but to keep him alive, otherwise he'll lose the Reaper's Game. Right before fighting the Game Master, he sees another flashback, this time going even further, seeing that the Game Master for that week himself killing Neku, and Joshua had shot the Game Master, suggesting that Joshua had tried to save him.
After Neku returns for week 3, he finds more and more evidence that one of the characters he had trusted for the entire game was the Composer, the ruler of Underground, and decides that the only way to come back to life, is to kill him. But when he arrives at his chamber, he finds that it was not him at all, and after defeating the Conductor, or head Reaper, he found that Joshua was the Composer all along, and Neku had been used to defeat the Conductor in an entirely new game, where the Conductor was trying to save Shibuya from being disposed of by Joshua. Not only that, but the flashback is completed, and it is revealed that Joshua had killed Neku to get him into the Underground. The character, who you had not only trusted for 2/3 of the game, but had been toying with the concept of being a traitor or not, had been using you, and turned the entire storyline on its head.