Scar Peter came from a future where Nathan hadn't been shot and had been able to give his full "First I was afraid, I was petrified, oh and btw lots of people have cool powers" speech. As a result of that speech, people in that world with powers were hunted and tested on. Scar Peter couldn't be doing with this, so he resolved to go back in time and shoot Nathan so the speech would never be made (avoid thinking about this logically or you'll realise he could've just gone back a few minutes before the speech started and explained everything to Nathan carefully).
So Scar Peter shoots Nathan. Naturally, normal Peter and Matt Parkman (Chief Wiggum) give chase. Unfortunately for them, Scar Peter just isn't in the mood to calmly explain everything (he was never as smart as he thought he was), so he sends Matt Parkman to the African desert where he can't do any harm... and hey, he might lose a few pounds. Scar Peter sends normal Peter to the company's prison cells. It's not clear yet, but he either changed Peter's appearance, or put his mind into the body of a prisoner named Jesse Fatface.
That's pretty much it. Of course, Angela Petrelli's droning on about how everyone else is doing everything wrong, but she's a stupid bitch anyway. Hard to say if she's really Sylar's mum.. I mean, we already saw the woman he thought was his mother (remember the snowglobes?). She's probably lying.