Shamelessly stolen from Iamthegamer over at GAF, but it's essentially the way I'm thinking:
ORIGINAL TIMELINE:
Claire Dies
Sylar blows up New York even though Hiro cut him, because Sylar can regnerate. Hiro finds that he can do this because Sylar consumed Claire's power.
time passes, the world is in turmoil BUT THAT'S ALL WE KNOW
NEW TIMELINE:
Hiro goes back in time after assembling the string theory (in the ORIGINAL TIMELINE), meeting with Peter at a specific time where all other things could fall into place so Sylar could be stopped from consuming Claire at the time he does, gives him the message, leaves.
Hiro returns, the future is still ****ed. He's only in Isaac's apartment for about a minute before the Hiro from the NEW TIMELINE affected by ORIGINAL TIMELINE Hiro's actions shows up. The events have changed (since in this timeline, Sylar still wasn't killed. He might've even gotten stronger). The bomb position has been transposed to Peter since Sylar's future was altered when not only did he fail to consume Claire's ability, but also by being caught by Bennet, thus delaying other things to occur.
Everything in the episode happens along this timeline
NEWEST TIMELINE:
New Timeline Hiro goes back to change the course once again, but will killing Sylar change anything? Why does Peter explode? These answers and more on your next episodes of Heroes!
