I posted a similar thread on the bennets, but realised that on that front it made sense. In that timeline, Peter had saved the cheerleader, but still exploded, claire alive, power not taken.

Yet, how come in that timeline, Sylar somehow managed to kill Nathan and Candice, fair enough.

But how come Sylar wasn't in New York for the explosion or Hiro stabbing him?

Actually, if you look back at the episode (my personal favorite, and I can quote a lot of it ), It never says he wasn't. Quite the opposite in fact.

Future Hiro gets excited when told Claire is alive and asks eagerly if Hiro killed Sylar. That implies that Future Hiro himself would still have stabbed Sylar. I see the Sylar line as not having changed much. He, or someone with interests in him (i.e., the Company) may have just dragged him into the sewer and things went from there. Fin.

Hope that helps a bit, and welcome to the boards!

but in that future, peter exploded and destroyed new york. That does not explain how Sylar wasn't blown up, let alone alive by being stabbed.

Several characters in that episode would still have been at Kirby Plaza when it blew. Nathan and Claire maybe not, because Nathan has been convinced by his mother, but all of the rest of them (Niki for example would have still gone to kill Linderman), so what's up with that?

In the original Dark Future, Claire was dead and Sylar regenerated after being stabbed and exploded. In the Five Years Gone future, which is the Dark Future that Claire wasn't killed, Peter was the bomb and Sylar was framed for the explosion.

ok, but that still doesn't explain how Sylar and Niki weren't at kirby plaza when peter exploded?

Re-read RiddlerHanjinome's response: Sylar likely would have been protected in the sewer.

Also, given Hiro's time jump to 5YG, the "butterfly effect" may have had him doing other things at the time, and other events which may have resulted in Niki NOT being in NY to rescue Micah from Linderman.