DR Jennifer:
A LAST-SEASON "HEROES" SPOILER
In the finale of season 1, Peter was about to go "nuclear" (this was after Hiro had stopped Siler). Nathan rushed over to him, embraced him and flew them into the sky. After some seconds we saw an enormous flash of light.
At the time, I had it in mind that they would NOT kill my favorite character on the show -- Peter, that is -- and devised a scenario in which he might survive, along with Nathan. That would have Nathan going as high as possible with Peter and then letting him go (Peter was starting to retain powers he absorbed from others and he would have gotten this from Claire).
As we saw, Nathan was a wreck. He abandoned his politics and apparently embarked upon a binge of self-recrimination. I have no idea why his wife would have left him, especially since she knew he was special and since she, herself, had been healed.
I wasn't at all surprised to see Peter at the end of the show. Relieved was more like it. But it must be one heck of a good story how he managed to be handcuffed in that shipping container. There is obviously a lot that has happened to both Petrellis that we will need to learn as the season goes forward.