Well the first thing I must point out is that nothing was definitively declared in actual dialogue on who died. Yes we saw the building explode with presumably Nikki inside. Yes we saw Nathan get shot and then we cut to the next scene with his mother on the phone, and in the background we hear the TV say that Nathan Petrelli was shot, but I do not recall actually hearing the words killed, murdered or assassinated. Oh and there is also Hiro burying Adam alive. Will he come back? Hmm.
Now all of this could be me just overanalyzing it, but honestly with the lazy writing that's been going on with Heroes this season, it doesn't seem too far fetched for the writers and producers to give themselves a creative "out" if they need it. But I digress…
At the end of the day, what really happened in this episode? Nikki saves Monica, sacrificing herself. Noah reveals to his family that he is alive only to leave them again so he can get back to work for The Company and they can have a normal life. Peter finally realizes, because of Nathan confronting him, that Adam is a bad guy and destroys the virus. Maya finally realizes, after him showing his true colors, that Sylar is a bad guy. Elle finds out Sylar is alive and goes to apprehend him hoping this will give her brownie points with her daddy, and in the process earns gratitude from Suresh, Molly, and Maya.
But now with the virus presumably destroyed and the skeletons in The Company's closet (or Safe if you prefer) finally seeing some light before Nathan got shot, how will the season pick up next year where it left off now?
Well right now all we have is time and plenty of it for the foreseeable future.