After discovering the horrible truth behind the Neo World Program in Danganronpa 2, Nagito sacrificed himself in order to kill the Remnants of Despair. He set up a "suicide" to cause Chiaki Nanami, the traitor and not a Remnant of Despair, to unknowingly deal the killing blow, and therefore become the blackened.

How did Chiaki accidentally kill Nagito?

In an attempt to stop a fire, Chiaki accidentally killed Nagito, due to his efforts to reveal the traitor. Chiaki told Hajime that she was the traitor and he was forced to prove this to everyone. ... Chiaki and Monomi were executed afterwards.

Who killed Nagito Komaeda death?

Nagito Komaeda: Killed by poison Chiaki Nanami accidentally threw.