I seriously didn't see Nathan actually letting his conscience win over. I knew it would be a good twist since Tim and his crew haven't disappointed me yet with the show, but that was just wow. It left so many questions too! Such as:

1.What happened to the hatian? He just disappeared as mentioned earlier in this thread.
2.Who is the man who can "see" Molly when she looks for him?
3.Was that trail of blood indicative that Sylar is still alive somehow?
4.How will Noah protect his family now? Especially since we don't even know what happened to his wife and son.
5.Was Peter still able to regenerate as was obvious he did in the nightmare future?

And plenty more, but I guess those are my top five for the time being. Still, even with all of that, I like the sense of closure that this brought. It really felt like a chapter has completed in the saga, and that they're ready to pick up with a whole new direction next season.

EDIT: Looks like Tim answered my question about Peter in the live blog.....sorta, and I guess I shouldn't be too surprised considering what a big role he played and all.

I just imagine Nathan and Peter in the air, Peter tells his brother "are you gonna blow?" he nods, Nathan lets him fall, flies away, far from him, avoiding the explosion. Everybody is safe and both Petrelli actor will still get a paycheck again for volume 2.

I'm greatly pleased that Niki has finally come into her own ability, which seems to be super-strength. It's likely that her sister, Jessica, had a power that enabled her consciousness to live on through someone else, and that Jessica would take control whenever Niki was about to discover her ability. This is how Niki was kept weak for so long. Good to see her attain a bit of inner peace.

It seems that D.L. won't be dying, and I doubt Parkman will kick off either. He's just too popular and wasn't introduced as a secondary character like Eden McCain or Ted Sprague, who both seemed destined to die.

Molly Walker is likely going to play a huge role in Season Two. They used her to do a little bit of foreshadowing, after all. Molly spoke of one person she can't find, someone who's so vile and corrupt that she can't even focus upon him without feeling the taint of his presence spying on her mind.
If you're at all familiar with the history of the X-Men, then this reminds me of the Shadow King. It's very likely that this entity will become the main villain of season two.

More and more, it also looks like Mama Pitrelli is the one pulling the strings. Though Linderman may have been powerful, Mama Pitrelli may have had a lot of influence upon the way he saw the future of mankind. After all, Mama Pitrelli was willing to sacrifice one child and corrupt another just to ensure NYC's destruction and more power for her family. Even the news of Linderman's death didn't seem to phase her, as if it was her own plan all along.

I kind of knew Nathan would come to save the day. You really don't introduce a reluctant character like that, with a power that seems tailor-made for emergency evacuations, and then proceed to NOT use him in the moment of need. Theoretically, Nathan could survive the blast if he lets Peter go at the right moment, then zooms out of the blast radius. I'm certain Nathan is plenty quick enough to catch Peter on the descent.

There is speculation as to whether Nathan will get to remain Congressman, should he survive. In the comics, Hana Gitelman is aware of the plot to rig the votes and takes it upon herself to unrig them, or expose the fraud. However, the TV series showed Nathan winning already, so it's unknown which course will prevail.

Hiro is just plain awesome. Teleporting all over the place and successfully impaling Sylar. The end scene was a bit of a shock, Hiro in feudal Japan, that is.
What's interesting is that it appeared to be George Takei under the ronin's mask, sporting the helix symbol, which is actually taken from adapted kanji characters (meaning it's a plausible thing for him to be carrying). Will suggested, two posts above, that Mr. Nakamura's ability might be extreme longevity. If this is so, then the legends of Kensei may be tales from Mr. Nakamura's own life.
I'm also waiting to find out if Hiro's sister will possess any skills. Hiro's father seems to favor her, so she may have manifested hers sooner, and with greater mastery.

There's a few loose ends: Whatever became of the Haitian Man, Claude Raines and Hana Gitelman? They just vanished (which is par for the course with Raines).

How, precisely, did Sylar learn to use other peoples' abilities? Did he eat their brains as Molly stated, or did he simply examine the DNA codons and instinctively alter his own to match?
And how did Sylar fake his own death while in the cell? Is this a power he picked up, or was it accomplished by studying the cockroach that repeatedly crawled nearby?

What of the older generation of Heroes? The comics have revealed that they were involved in Vietnam War maneuvers, as soldiers. Linderman was a field medic and Mr. Pitrelli was in the platoon. There have been other heroes associated with them, namely Mr. Nakamura, Mama Pitrelli and Mr. Deveaux. There's obviously a backstory there and I really hope it's revealed in Season two.

I figured they'd also leave it unknown as to whether Sylar was actually killed. The trail of blood makes it look like he either crawled to the sewers, or something dragged his corpse.

On the plus side, Ando remained alive, and Mr. Bennett finally got a first name: Noah. 'Bout time. I expect him to be a rather integral resistance figure in the next season or two.

The manhole beside Sylar didn't look like it had been moved enough for him to have crawled through it, and even if he managed that there's no way he had enough strength to climb down. I'm wondering if there was more to the melting guy's ability that Sylar stole. We haven't seen him use it since then, and it's plausible that he could have slowly liquified himself as he got to the manhole. Once down there he could have figured out how to re-solidify. So little time was spent on that ability, unlike his super hearing acquired around the same time, that we don't know if it can be used like that.

I'm a little doubtful that he could have escaped at all though. It seemed to suggest it, but there were too many people there who would have noticed the disappearance of Sylar's body.

I suppose anything is possible at this point, but I don't think his power allowed him to melt anything that wasn't composed of metal.

I kinda always thought of the possibility to just fly away and explode far, far up in the sky instead of doing it in the city. It was just too obvious and I was kinda hoping that they would solve it some other way. Peter already had the power of flight since it was one of the first abilities he "stole", but it turns out that his brother was there to save him in the end after all.

This brings me up to a theory, or rather, a question, about Peter's powers:

Is Peter able to use more than one power at once? If he isn't, that would explain why he didn't fly away by himself. Has he ever used more than one ability at a time? I don't remember...

Actually, I was a little flumoxed by Peter's explosion. If it was an atomic explosion equivalent to a nuclear bomb (and Sprague's radiation would indicate that), wouldn't exploding over New York City shower the populace with fallout? Also, if you look directly at a nuclear blast, can't it burn out your retinas the same as looking at the sun for too long?

I thought if it was detonated up high enough then EMP was the only real danger. I had the same thought as Aardark on that. If nothing else, perhaps Sprague's radiation is a bit different since no one on the outskirts of the explosion in "5 Years Later" seemed mutated or sick. That would've been plenty of time to see the full effects if it had caused any birth defects and such.

As for retina burning, shouldn't it have blinded Hiro and some of those feudal soldiers to stare directly at the eclipse too? Maybe "special" people all have ultra-durable eyes.

Maybe "the bomb" was sort of like Midas from Front Mission 3 (i.e. environment-friendly). The only reason I even had that in mind is that my buddy put on a Discovery special on atomic weaponry after the 24 finale but before I went home and watched Heroes. Doesn't the EMP have something to do with how high it goes off? If it were high enough, it shouldn't be a problem. Damn, I wish I had been paying more attention to the special. XD

Crash, at first glance I could've sworn it was George in the Samurai getup. But then I slowed it down (DVR <3) and I wasn't convinced. But I'll bet anything that the eyes under that helmet were the same reflected in George's sword during the previous episode. I'm totally sold on the longevity thing now. Being alive for that long would explain his skill, knowledge, and influence.

I'm interested in the powers of the older characters more than ever, and it looks like they'll play a bigger part in Volume 2. I'm especially intrigued by Peter's vision of Simone's father.

I don't think it's particularly likely, especially given his limited role in the bastard future, but might the Hatian be the one Molly can't find, the one that can see her when she looks for him?

I stand corrected. Nuclear fallout comes from the radioactive debris kicked up from the explosion, so if it exploded in midair, then there's no fallout. As for the blindness, most likely they would have experienced temporary blindness for 3-10 minutes, but that's about the worst that could have happened.