I think there actually may be a smoking gun that reveals what will happen next year and puts into perspective the events that occurred during the season finale. I've seen it hinted at before in a post, but I didn't see anyone jump to the conclusion that I jumped to, so I decided to create this thread Proceed with caution if you don't want any possibility of a major Heroes plot being spoiled.
During the Final segment after Sylar is defeated, Claire is struggling with the thought of killing Peter, and the following conversation takes place:
Peter: Do it. Do it! You're the only one, Claire.
Claire: Tell me theres another way, please.
Peter: Shoot me. There is no other way.
Nathan[
Flys-In]: Yes there is, Claire.
And as we know, Nathan decides to make the biggest sacrifice, saving New York by flying Peter into the sky and exposing himself to deadly radiation and likely his death.
But did you notice something? how about the bolded portion of the conversation. NATHAN IS FLYING IN WHEN THE CONVERSATION IS TAKING PLACE! How could he have possibly of heard the conversation that was going on between Claire and Peter, they weren't exactly shouting loud enough for someone thousands of feet in the air to hear them. And that's where the smoking gun known as super hearing comes in, and who's holding that smoking gun but none other than everyone's favorite watchmaker.
Doing my best Monk impression... Here's what happened:
Remember what Molly said to Mohinder about Sylar when Mohinder asked if Sylar was on his way? She said that he was already there. You know who else was already there? Candice, who as we all know, has the power of illusion. Sylar had ample time to take her power, which means he could take any form he wanted. This is the power that sets the rest of Sylar's plan into motion.
The first form he takes is as Claire. A repentant Nathan flies to the scene where the exploding man is supposed to detonate, in hopes of finding his brother there. He finds Claire(or so he thinks) and goes with her to try and find Peter. The search doesn't last long, as he ends up getting his brains munched by Sylar because he let his guard down.
The second thing Sylar does, is use the illusionary power to pull the wool completely over everyone's eyes. Sylar gets stabbed and killed by Hiro, and everyone thinks that the dangerous psychopath has finally been defeated. But truthfully Sylar either used a clone, or illusioned that he was stabbed when he really had dodged the attack. he illusions his own death, so that no one expects the plot that he's putting in place is happening.
The next and final major form that Sylar takes is that of Nathan. He uses Nathan's flight power to get Peter right where he needs him to be: in the sky, all alone. Peter can't fight back since he's about to explode, and since no one can see what's happening in the sky, Sylar can munch on some more Petrelli Brains.
The bomb that goes off is Sylar using Ted's power. But all the heroes think it was Peter who exploded, and won't be suprised when they learn that Peter won't be returning.
The people of New York will want to know what the large explosion was in the sky that night, and this is when Sylar takes the form of a charred and disfigured Nathan, who tells the world what happened that day. The congressman will be applauded for his bravery, and pitied for the death of his brother. The world will grow to accept people with abilities, but Sylar(as Nathan) will stress that even the most peaceful of people can be dangerous if they have abilities, and point to Peter Petrelli as the ultimate example. Because of the sacrifices that the world thinks Nathan Petrelli has made, they will elect him into the presidency. They will follow his plan to "help" people with abilities, but as we all know there is no way to help them, Sylar will just be helping himself to the all-you-can-eat special at the brain buffet. Sylar will realize his mother's wish for him to be special, and be as close as he possibly can be to being able to taste the most delicious brains of them all: cheerleader brains. What they lack in quantity they make up for in flavor.
Of course, with new york being spared destruction, the heroes that died in New York will still be alive, unlike in the episode 5 years gone. Micah will be alive, meaning his manipulation of machines is still on the table and Nikki has access to Jessica's powers(never learned to control them in 5 years gone). Hiro won't become cynical because of Ando's death, and then there's the issue of the only man that Molly is afraid of trying to find. We didn't see him in 5 years gone, perhaps he too died in the explosion? or perhaps never had a reason to reveal himself.
Point is, even though Sylar gets in control, the events of 5 years gone aren't a certainty, who knows what can happen. the creative team working for Heroes could likely form endless outcomes for this scenario that didn't involve Sylar getting Indestructibility.
Oh, if you're not covinced that this may be what actually happens, here's some more evidence for my theory. take this conversation between Noah and Peter as they enter the scene where the exploding man is supposed to detonate. They're looking for Sylar.
Peter

oesn't look like there are many places to hide, are you sure about this tracking system?
Noah: He's here, don't worry.
Peter: Alright, look, alright, then that means he's
hiding in plain sight
When Peter says that last line, he's looking directly at Noah. he turns to face the same direction as Noah for just a split second, and Sylar sneaks up and taps Noah on the shoulder, tossing him into a wall. How could Peter have not seen him? the Sylar we know shouldn't be able to pull that off, but with the illusion ability or the ability to fly at the speed of sound, appearing in a place in a split second is very plausible.
Now, the evidence I pointed out could have just been mistakes made by the people producing Heroes, but those are some awfully odd mistakes for them to make, they haven't made those types of mistakes before. It all fits into place, and would be an outstanding story. This allows the actor who portrays Nathan to stay on the show for a while, while Zachary Quinto takes a brief leave from the series, as he is presumed dead. When the truth is finally revealed on the show, many fans will be shocked, and the show will point out these small details that many had overlooked during the season one finale. The fans that questioned the way the season ended the way it did, would be applauding the creative staff's decision if this is what really happens.