I think that Peter is retaining some of the powers... don't know how much though. Hell, I could be wrong though.
Maybe all the heroes know that since Peter has the ability to use their powers... and we saw in his "dream" of the future, that Claire mouthed "Im sorry" that they all HAD to be within that area, to overload him with powers... to take out Nathan? Nathan walked out the door, and right toward his brother. Maybe Nathan is a bad guy.
Did you look at the latest comic story they put up? It's Mr. Bennett, going to Eden's father, to let him know that his daughter is dead. He tells that S.O.B. that she gave her life to keep a depraved and dangerous man from gaining her GIFT. Her sacrifice will save millions of lives... and that she's a hero. They show what happened after Eden died (because they didn't show us in the show, and I was left sitting there, wondering what happened to Sylar, and if he escaped). They came in and shot him, with a crap load of needle darts (drugs, I assume) and knocked him out. After Mr Bennett leaves the house where Eden's father is, the Haitian man is told to erase everything but the guilt.... because of what he did to his daughter as a child.
So, we know they they still have Sylar. Only thing is.. WHAT are they keeping him alive for?