To cut to the chase: Sylar kills Nathan, Peter (shape shifting as the President) knocks out Sylar (shape shifting as Nathan), Angela convinces Matt to implant in Sylar's mind that he really is Nathan. HRG sees and approves this.
So Season 3 ends with some hope, but on shifting sands. HRG and Angela will have to lie to Claire and Peter - a satisfying plot turn, since they were lied to for most of the first season. Matt will have to lie, too, if he's brought into this again.
And will Sylar's conversion to Nathan really hold? In the brief beginning we see of Season 4, Nathan is beginning to take an interest in the workings of clocks...
The other big question mark at the end of Season 3 is what will happen to Hiro and his powers? They're beginning to make his body sick. Mohinder tells Hiro he better not be stopping time any more .... But, of course, Hiro does, at least once, and you know he will be sorely tempted to do it again.
This was an interesting, transitional season for Heroes. It still has not regained the sheer sense of wonder of the first season, but it is pulling itself up, slowly, thoughtfully, not easily, to an older, more contemplative kind of show.
Zachary Quinto may not have as big a role as Sylar looking like Sylar next season. That might well be to the good, since I expect the new Star Trek movie to be an enormous success, which will make Quinto more evocative of Spock than Sylar. And Ali Larter will be back in some sort of role next season, which is all to the good, too.
I'll definitely be watching.
See also Heroes Gets Lost ... Heroes 3 Begins: Best Yet, Riddled with Time Travel and Paradox ... Sylar's Redemption and other Heroes and Villains Mergers ... Costa Nuclear ... Hearts of Gold and the Debased ... Seeing the Future Trumps Time Travel ... Superpowered Chess with Shifting Pieces ... Villains and Backstories ... The Redemption of Sylar ... Thoughts on the Eclipse, Part I ... The Lore of the Comic Book Store ... Hiro's Time Traveling Closure ... Augmented ... Shades of Recalibration ... Baby, Rebel, and Last Fantasy ... All that Shape Changes Remains the Same?