( Molly ) Sylar did kill Nathan, but not to impersonate him. It was back in DC, several months ago.
Peter incapacitated him, and Mrs. Petrelli couldn't cope with the fact that Nathan was dead. She told Matt Parkman to wipe Sylar's mind completely and make him believe he was Nathan Petrelli. His shapeshifting and clairsentience took care of the rest. I didn't agree with it, but Angela was in pain and I let my emotions cloud my judgement.
We were wrong to do what we did, but the situation is complicated now, more than before. The people here need Nathan, and if he ever remembers who he really is, he could be a real threat.