After Peter took the Haitian's ability, he confronted Sylar, erased his powers and almost beat him to death. As a result - somehow - Nathan once again emerged. The brothers chatted and bonded and Nathan admitted that the attempts to fight off Sylar were killing him.
When Peter took his sibling to the same rooftop we saw on season one, Nathan ran to the ledge and jumped off. Peter grabbed him by the hand, but he knew it was over. Nathan gave him a speech about remaining a force for good in the world and dropped to his death. After his body bounced off a car, it stood up and walked... but not it was truly Sylar again.
Elsewhere, we met a carnie named Eli. He's a multiplier and can create multiple versions of himself. He broke into HRG's house and stole his box of Primatech files.
Claire and Gretchen made it to the carnival. Samuel greeted them warmly and showed them around his creation and introduced them to his family. Claire was taken by a place where people with abilities were accepted and out in the open. When Gretchen left to go back to school, Claire stayed behind and was present when Samuel gave a speech to his family about recruiting more heroes in order to assert their dominance and no longer live in fear.
With that speech, the show faded to black and Heroes took a hiatus until January 2010.
Source: TV Fanatic