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Originally Posted by blankall
Peter choses to have that scar. W/ Claires powers he could easily regenerate, but instead chose to allow himself to heal normally so there would be a scar. My guess is he gained it at or around the time of his explosion. He wears it to reflect his new darker personality caused by this event.
Savind the chearleader was only part of the puzzle. Sylar was the original one who blew up NYC, but w/out claire's powers he is not bold enough to do it. This leaves space for Linderman to do it instead.
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Here's my theory, although I'm sure it's going to have plotholes because of the complexity of the series.
In the future timeline, Peter DOESN'T gain the ability to regenerate, hence the scar on his face (and the fact that we didn't see him use his regenerative powers in
Five Years Gone). He did not save Claire from Sylar in the past, and thus did not sponge her powers, but somehow Claire still survived. Perhaps we do not see Momma Petrelli in the future because Sylar has killed her too, and her unknown power, based on bloodline, was also regeneration (In addition, he might have been able to kill Linderman as well, which would help explain Nathan Petrelli's death too, and realize his potential for political power).
When doomsday came, Peter and Sylar squared off in New York City, and this is where Peter receives the slash on his face. Hiro catches Sylar by surprise and stabs him (as per the Comic Book), but realizes it does no good to Sylar. Before Sylar can kill Hiro, Hiro tells Peter he can save the world all over again via time travel, and Hiro time travels out of New York, but accidentally leaves Ando behind. Peter and Sylar continue fighting, and Peter becomes no match for him. However, before Peter dies, he absorbs Sylar's power that Sylar stole from Claire/Momma Petrelli/Linderman, and thus realizes that his newfound ability would enable him to destroy Sylar permanently and regenerate. Knowing that Hiro exists in the future and has the ability to time travel, Peters decides there is only one way to permanently destroy Sylar. At this moment, Peter combusts, and destroys NYC. Both Peter and Sylar are able to survive the blast, and escape the aftermath from each other. Hiro returns to the scene, finds Ando and millions others are dead, and vows to return to the past to prevent Sylar from letting this happen.
The other characters are not present in New York at the time of the blast, because their deaths in a huge explosion would prevent Sylar from taking their powers, such as D.L.'s phasing and Candice's illusion powers. The next season shows that the explosion actually happened, and thus the events that follow are Peter blaming himself for the explosion and going into recluse, Sylar determined to wax the rest of the protagonists and take political power, Hiro's devotion to preventing the past, and Suresh and all the other characters helping find others to stop Sylar (hence the introduction of Molly Walker).
That's just my two cents. For those who are fans, the original plot has shades of Dragonball written all over it, especially the Cell saga. It's likely this is where the writers got some inspiration for the series.