Here's a few things...pure speculation, so I don't think they're spoilers...well, I'll be safe.
[Sblock=Speculations]Peter came into contact with Niki/Jessica at the end of Season 1. Suppose that "mirror split" thing isn't just Niki's MPD...suppose Jessica (as was vaguely hinted at) really IS somehow a different person? Niki's sister, who died...but managed to live in her sister's reflection/soul? Does that mean Peter absorbed that? If so, what happens if Peter dies...then regenerates back to life? Mirror Peter (who exists as he was before he regenerated) and Original Peter (who came back to life and healed himself...then either got mindwiped
or accidentally mindwiped himself after absorbing Haitian's power)? Or maybe he lacks his memory because his memory -is in the reflection-?
Mew.
Another possibility. This one is...more farfetched. What if Nathan's power isn't really flying? Maybe he's more like Peter. He might have gotten flying from a brush with someone else (did he ever live in Costa Verde?
), but for some reason his power to absorb might be more limited, or have a worse mental block than Peter's did... But then when Peter blew, he got access to the other powers he absorbed. So he didn't die...etc etc...
If the face in the mirror is Nathan, it's hard to see how it's happening. It can't JUST be a disguise. That kind of severe burn would at the very least have him in agony and require constant treatment and anti-infection therapy and skin grafts. More likely it would be fatal. All I can figure is that Nathan took Peter up...and Peter used Hiro's power to teleport away or something. Nathan's therefore guilty because he -intended- to die heroically...but instead his brother, the noble one, died and he couldn't save him. He was denied the redemption he sought...the redemption he needed for having ever gone along with Linderman's, and his mother's, plan.
...he may be trying to get that redemption now via other means. Muahahaha.
Edit: Oh no...I think I know! Super Secret Speculation:
PETER is the Hooded Man...in Nathan's body! Burned, Bitter, Dead Peter...tainted by rage, taking out those who plotted not only HIS demise, but the death of millions!
Interestingly, redemption is something Mr. Nakamura also mentioned. Perhaps this season isn't about becoming a hero (as last season was) but rather about the redemption of heros.[/sblock]