When I was watching this episode I started thinking about all of the different time lines could tie together and why it was that Peter was considered so special that the Observers not even tried to "right the wrong" of saving Peter but go as far as to have September decide NOT to eliminate him from the timeline when he was requested to do so. Let's look back to some of the original story lines!
In our first, primary story line we have the story of a boy born with a genetic disease that was destined to kill him, removing him from the time line. This event caused his father, a scientist, to use his abilities to create a way to peer into another universe. This eye into Pandora's box began as a simple measure of trying to save his child, but soon emotions took over when he noticed the Observer prevent Walternate from noticing the cure for his child. This emotional reaction caused Walter to open Pandora's box, moving between universes only to steal something that should not belong in his universe. As we saw throughout our interactions with the Observers they appeared only interested in those individuals deemed "important." Although we have still not understood what "important" means, there was most definitely something important about Peter. Peter's presence in this world brought forth destruction to the universe from which he was pulled, and further brought effective Armageddon against Walter's universe. And so we come to the machine, a creation not of this world that was capable of both creation and destruction. As we see in the episode "The Day We All Died" it appears that the machine was in fact sent back in pieces by our Fringe team in hopes that Peter's consciousness during his time in the machine would have the thoughts capable to bringing the two universes together, temporarily saving both from destruction. After this occurrence Peter disappears from the timeline as the worlds begin to heal and the effects of his kidnapping begin to resolve. It's also important to note that Olivia does die in the end of this potential timeline.
In the next timeline Peter's "essence" is apparently trapped. He is trying desperately to escape wherever he might be, and we find that as he comes to be in the new timeline that he isn't recognized. He never existed. September is ordered to eliminate Peter from the timeline before his essence can become a reality. We see him make a decision to not eliminate Peter at the last moment. As this story line unfolds we find that the Observers become increasingly more concerned in the condition of the two universes, and the peculiarity that is Peter Bishop becomes even more evident. When Peter makes a decision to shut down the machine the two worlds are once again separated leaving the "altiverse" to die from the corruption of the imbalance of nature. This becomes a bit more complex as Bell decides to create a brand new universe. September gives a warning to Olivia about having to die in the end of it all. As we come to find out this means that Olivia had to die in order to save the worlds from collapsing on one another to create Bell's utopia. This gives Peter and Walter a great sense of loss, and in this sense of emotional overhaul they manage to revive Olivia, seemingly preventing the words of September from coming to be true. As the team returns home we are left with the realization that the primary world will go on while the altiverse is left to rot into oblivion. Also during this timeline we get a glance into the mind of an Observer. We see how they exist between timelines and how the "universe" was taken from him for what happened to him. This is also how Peter is given clues to free September from his prison. We are also introduced to the idea that Observers exist as some sort of future, super humans that empower themselves with some form of tech. As the season comes to an end September appears to inform everyone that the rest of the Observers are coming.
So, why do the Observers care? I've actually thought about this in two different ways. Let's go with the more likely of the two, yet the least interesting. The future world of the Observers is one that exists in a world after the destruction brought forth by Peter Bishops life events. They have come back in time to observe events they felt important as a way of studying what happened to lead to a dying world. They realize that the source of this corruption is that of Peter, and their mission after Peter is saved is to effectively "right the wrong" that September created. September is continually instructed to eliminate Peter from the timeline. As a relationship with Olivia is built by Peter we see that she begins to be a focus of the Observers. It's like the Observers recognize that through her he's the weakest because of the emotion of love, and this is further shown to be true when Etta is killed by December. He makes a mention that they will return because of love. In "The Day We All Died" Olivia is killed shortly before Walter and Peter make the decision to send back the pieces of the machine through a wormhole. I believe Peter assumes the technology of the observers to basically do what we all expect -- use the technology to gain an equal footing so that we can actually save the world. At some point we will come across September, and he will very likely play a huge role in the end of the world. "You don't even know what you don't know." This probably relates to a lot of things. Often, people can say "this is something I don't know anything about." With the Observers present there are a number of variables that Peter has no knowledge. He is, in fact, ignorant. By assuming this technology he will begin to understand that which he doesn't even realize could exist, and in return become aware of that which he does not know. This is the beginning of knowledge. Once you understand what you do not know you can then move towards understanding how to learn it. I believe in time that Peter's new found powers will become a key portion of the final plan by Walter and September.
Now, for a darker twist...
Let's assume that Peter's use of the technology eventually corrupts him. Let's say that Peter uses this technology to save the world from an onslaught of invaders. As we've seen the Bishop family messes in Fringe science. Peter will recognize the importance of a technology like his, and they will find a way to mass produce it as a way to better humanity. Perhaps this technology will be necessary in part to help save the world or at least its people from the after effects of the Observers' corruption with the degradation systems and whatnot. In this train of thought perhaps then Peter eventually begins the evolutionary process of the post-human era. These scientists, as they call themselves, will be selected and amplified to help with a program to possibly return the world to how it once was. We begin to use this future technology to save our world. This begins a vicious cycle in which what we are already seeing happen begins again. Peter indirectly begins the process that leads to the creation of the Observers, and their rise to power in the future. If this were true then the future Observers could actually be a resistance group looking back through time trying to see how the corruption began thus identifying Peter as the source of it all. Their decision to make up for Peter's existence, even to go as far as to order killing him, shows that they wish to prevent whatever hell their future is. Again, we don't even know what we don't know. If this is true then September would be actually an evil entity instead of the hero he appears. His decisions to not eliminate Peter and/or save him shows that he wishes for this cycle to continue. Remember, in all other timelines we've seen that Peter has made a decision that ultimately affected the way the world turned out. He made decisions that determined if an entire universe would live or die. What's to say that he doesn't ultimately use his desire to save to create a team to see that it will work. We do have the technology now, don't we? I wouldn't argue that he becomes an Observer, but it is possible he does start the fall of the Dominoes that would lead to their creation. TL;DR: Peter being eliminated might actually have prevented the invasion from ever happening.
http://fringe-forum.com/forums/show...-September-!-!&p=374377&viewfull=1#post374377