I think we're starting to get somewhere! Hiro has finished whatever he set out to do in ancient Japan but not without really pissing off the English guy that speaks Japanese, let's call him Adam. So Hiro thinks he saved the world, but we see that Peter has found out there is a new threat looming over mankind - a plague.
Peter has all these super powers but has amnesia and doesn't know how to use them. So he moves in time, just like Hiro, but into the future. Dragging his new Australian girlfriend with him. New York looks deserted until the military shows up and takes them to a decontamination facility. There is where Peters mother shows up but he doesn't know her. She commands him to remember and to save the world. Now if that woman told me to do something I'd do it too. Poor Peter, the first thing he remembers is probably the one thing he's wants to never remember and that's dear ol' mom. She gives me shivers. Peter moves in time again, oh and leaving his new Australian girlfriend in the future, she really knows how to pick em, huh?
We find out that Matt's dad The Nightmare Man isn't the really bad guy, he's a puppet of Adam, the really, really bad guy, you see where I'm going with this? Adam escaped 2 weeks ago and is killing everyone in that picture.
We see Peter in a room trying to figure out where he is and trying to move in time again when someone comes to the door, opens it, Peter shoots an electric fireball at him, it hits his hand and he heals! Oh it's the English guy that speaks Japanese and was in ancient Japan with Hiro. He says, "Peter what are you doing?"
Peter asks, "Who are you?"
And the English guy that speaks Japanese and was in ancient Japan with Hiro says, "It's me Adam."