As mentioned Future Peter, unlike Future Hiro, didn't consider that altering the past to keep Nathan from coming out would lead to such devastating consequences. Because of what he did, Sylar obtained Claire's power and almost a dozen major captives with dangerous powers were set free. In all likelihood the future Future Peter's created is far worse than the one he tried to stop in the first place. After all, wouldn't he disappear if the dark future was averted, negating his reason for being there? Of course it isn't until after that he begins to craft a time line like Future Hiro did in Isaac's loft (guess Peter hasn't gotten much smarter in the interim four years).
This alternate timeline is brought up in Matt's trek in Africa, where a man named Usutu (played by Ntare Guma Mbaho Mwine, who was cut from the original pilot playing a different character) tells him that the future he saw is now contradicted by Matt being there. He can serve much like Isaac did down to the painting, only this time Usutu is far better aware of the details of his visions (like names). Of course it isn't a coincidence that his painting of a world breaking along a line similar to the Symbol is on a rock in Africa as well as a pier in New York City, but how exactly did that happen?
Mohinder is also seeing repercussions in his research. While at first he becomes basically Spider-Man without the webbing, it turns out there is no free lunch as his skin begins to peel off in chunks. His behavior is far more aggressive and primal throughout the episode, which may indicate the serum is making him more like an animal.
Towards the end of season two, Elle realized how exploited and poorly treated she was her whole life, especially compared to Claire. She's needed validation and in that selfish pursuit, became a hero by saving Mohinder, Maya and Molly (alliteration!) from Sylar. It seemed like that would've been the rest of her arc had the season continued (Kristen Bell was signed for more episodes than Heroes produced last season). Here, it seems like they are continuing that, as Bob reprimands her for letting Sylar get away, and for good reason as we see later in the episode, then as Angela fires her as she lost her protection in The Company. She's been trying to prove herself, and maybe will find an outlet for that finding the escaped villains alone, or with Bennet.
During her attack, Claire remarked that she felt no pain. Afterwards she spends the episode in a state of shock, unable to feel anything and wondering what that means. As she's mentioned, she felt pain, even if it was momentary as the wounds quickly healed. The shutting down of her nerves could be psychological, but maybe Sylar, knowing how the brain operates, flipped a switch inside her brain to turn it off as a way of further manipulation, or to keep her from screaming.
Tracy's story begins to take shape with the obvious follow up of her resembling Niki. Nathan mentions it and in a nice call back, the investigating journalist uncovered the surveillance footage of Jessica and Nathan as well as Niki's website. While we've been lead to assume they're the same person, Tracy freezing the journalist is enough proof for us to assume that they are two different people. The two main theories are that either Tracy is the real Jessica, who didn't die as believed and has a power and multiple personalities like her sister or that Tracy is a clone. I'd rather believe the former, as the latter may be rejected by the audience as a little too much.
With his resources, Hiro identifies the Speedster as Daphne, a woman living in Paris with a lot of expensive junk and no place to put it. Hiro's plan to trade one of her prized medals for the formula reveals the rift beginning between himself and Ando. Of course, seeing a vision of your friend electrocuting you is going to lead to some awkwardness. While it may be easy to say Hiro isn't being fair, the extremity of the vision is enough to explain it. It doesn't justify telling Ando that he went bad. The scene is clearly ambiguous as to which one turned, but Hiro can't be unbiased.
However, Hiro still stands by his friend when Daphne threatens Ando at knifepoint, knowing he has a way around Daphne's super speed making her difficult to locate. Hiro's smart enough to place a tracking device on it, leading them to her location somewhere in Germany. There are plenty of intriguing elements to this, such as who is Daphne's boss, does he/she have the other half and why are they interested in getting it (not to mention Why Germany?)
If the premiere is an indicator, Angela is going to be a huge player in this volume (Cristine Rose has been promoted to series regular). All the major threats so far have stemmed from what Angela and her eleven associates did thirty years prior, but this time Angela's taking a more active role earlier in the game. She finally reveals her power: precognitive dreaming which was Peter's first absorbed power, and makes a power play by trying to put Sylar under her thumb.
Angela's dream is rather graphic, a return to the more grisly imagery of the series' early episodes, where all our heroes are torn apart so much so that not even Peter can recover. In it the rogue gallery includes Knox, an awake Maury Parkman, an unburied Adam and an undetermined character played by Ali Larter. Since both major villains from season two weren't killed off, they must've computed that in anticipation for this.
An interesting theory stemming from Maury's cameo is that he is influencing Nathan by showing Linderman to him only. It shouldn't be a big surprise that Linderman has been an illusion all along, but why and how considering when we last saw him? The Maury theory may be the strongest to date, but it still doesn't explain how Nathan was able to heal from who should've been two fatal gunshot wounds.
There are some questions about Peter's predicament in Jesse's body that will likely be answered soon. What happened to the real Jesse? Did he get "hollowed out" and Peter was thrown in? Do Peter's powers still work and is he collecting the powers of the escapees with him?
There is one major problem with the rogue gallery: "The German" who can control magnetic fields. Seriously? I'm admittedly not well-versed in comics but even I know that's obviously too close to X-Men's Magneto.
And why did they let the pyrokinetic guy burn a woman to death not two yards away from the gas pump? One flame gets too close and they get in the worst gas pump explosion since Zoolander.
The other problem I have is with the reveal that Angela is Sylar's real mother. The secret twist familial relationship has been done so many times, especially in soaps, that for it not to induce eye rolling they need to earn it. A great recent example of one that did is the first season of Dexter, which used a shocking family connection effectively since it was hinted at and alluded to throughout the first season and makes sense when rewatching those episodes. This almost sounds like fan fiction. However, they could easily make up for that shortcoming, like if this is Angela's attempt to manipulate Sylar, since physical torture isn't going to do much now.
Bennet ends the episode with a new mission: to bag and tag the eleven other escapees again. Unfortunately Bennet had little to do in this premiere, which is strange considering he's one of the series' best assets. However, Bennet is on a mission and out to punish someone who hurt Claire, and when is that not entertaining?
Regardless of the nitpicks, this premiere was a solid effort and this one improved upon the first hour. Yes there are plenty of plot holes (as I've mentioned), but this felt as fun as an average first season episode and that's a good indicator. The ratings, unfortunately, were down, but if the episodes maintain and eventually improve on this quality, Heroes could get its buzz back.