Nathan was killed by Sylar in the episode "An Invisible Thread". At Angela and Noah's urging to keep Nathan "alive" for the sake of their family (themselves, Peter, and Claire - the latter two who are kept unaware of Nathan's death at this time) and to shut down the government operation now controlled by Danko, Matt transformed Sylar into Nathan in order to tell the President this operation was a mistake. After shape-shifting Sylar into Nathan's form, Matt transformed Sylar into Nathan by filling him with Nathan's persona and memories. However, in volume five, once Nathan becomes aware of what happened and realizes he is stuck in Sylar's body, Nathan accepts his death in episode, "The Fifth Stage."