In an alternate past, Nathan was allowed to finish his speech. He was then furiously hunted by the company. After months on the run (assisted by his ability) he finally realises it was not a good idea. He seeks Peter to transport him back into the past and shoot his past self.
The most likely perpatrators are Adam Monroe - but he was buried at the time, HRG - to save Claire, Bob - not the type to put himself at risk, A person employed by Angela Petrelli - "Pandora's box has been opened".

