Here’s my theory.
Future Hiro and pals believed that Syler had cause the explosion. In fact, it was Peter who exploded and destroyed the city. Syler, who was disguised as Nathan at this point, helped spread the story that Syler caused the explosion and was killed in the process. Presumably only Syler and Peter know the truth. Syler must have found and killed Candice at some point and absorbed her illusion powers.
Claire was not killed by Syler, though everyone believes she was. Mr. Bennet did an admirably good job of hiding her and convincing everyone that she was dead. Therefore Syler never acquired her regeneration powers. When Claire was finally captured and brought to Nathan/Syler, he said something along the lines of “waited a long time for this” as he did the head-opening thing on her. Implying that he’d wanted her power for a while but never managed to get it.
Peter picks up the powers of anyone near him. Frequently when he first picks up a power he’ll start manifesting it uncontrollably and often without even realizing he’s doing so. He has only just learned to intentionally manifest powers, but hasn’t had any training in how to stop from manifesting new powers as soon as he acquires them.
Future Hiro claimed that he had stabbed Syler in an attempt to stop him from destroying the city, but that Syler then regenerated. But Syler didn’t have the regeneration power, nor was he the one who exploded and destroyed the city. Peter is the only one with the ability to both regenerate and explode that we know.
My theory is that Hiro never stabs Syler at all. Hiro stabs Peter who is unintentionally appearing to be Syler as a result of just having picked up Candice’s illusion power. Peter, who has had Claire’s regeneration power for some time, heals from the stab wound, and then soon after picks up Ted’s radiation powers and explodes. Hiro becomes convinced that he failed to stop Syler from destroying the city because Syler had killed Claire and taken her power, when in fact Syler was never the cause of the explosion.
Erroneously convinced that preventing Syler from killing Claire is the key to stopping the explosion, Future Hiro travels back and tells Peter to save Claire, thus insuring that Peter will pick up Claire’s power, survive being stabbed, and destroy the city. “Save the Cheerleader, Save the World” is in fact exactly the wrong advice, being based on false information about the actual cause of the explosion.
If my theory is true, then at this point everything is still exactly on course for the explosion. Peter is still in the city, having Claire’s regeneration power and quite likely to run into Candice and Ted in the near future. Hiro has been sent back with the firm instruction to find Syler and stab him. Linderman is still pulling strings to get Nathan elected. And Syler, having now taken Issac’s future-seeing power, knows exactly what he needs to do to take advantage of the situation.