Ok, so let's analyze the show a bit after the revelations in the last episode..

September:

1. Saves the boy, changes the timeline, creates the beginning of everything we have seen, season 1-5, Peter is the key to it all, and he's the start of September's interference.

2. I'm going to go with September also being the reason Walter ended up removing parts of his brain.. we have seen flashes of egotistical Walter, I just don't believe he would have willingly taken out that knowledge without a push from someone.. namely - September.

3. September brings Walter back to the grave sight of his real son in the season finale of season 1, bringing knowledge once thought lost, back into Walter's brain about the "other side." This knowledge, along with Olivia meeting Bell on the other side allow for the events of season 2 to take place. (I believe Walter having knowledge of events in the past, allowed for "Bell's plans" to manifest themselves in such a way that it actually ended up being "Septembers plan" throughout the entirety of season 2)

4. Which brings us to "Over There (part 1)" when September hands a very upset and distrot Walter the blueprints to the "machine", a machine btw, that they wont even start building til mid-season 3, but this alone gives Walter the drive to get his act in gear to get Peter back to this side, simply because Henry was never to be born.. he did NOT fit into September's plan.

5. Does matter, Walternate sends the other Olivia over, causing Henry to still be born, we know the Observers wanted Henry to exist because they were watching everything transpire "over there" with Henry, and possibly even helped to facilitate the "fast birth" because they did not want the other Olivia to die.

6. All the while our Fringe team is building the machine from the blueprints, given to them by September (think about this.. had September never given them the blueprints, we would have had Henry, and only the other side), Sam Weiss tells Nina that whichever Olivia, Peter chooses will be the side that is saved, this leads me to believe that this information came direction from the manuscript.

I truly believe the "perfect" outcome of season 3 for the Observers would have been for Peter to chose the other side, have Henry, and stay over there - with a group that would have never been able to stop the Observer invasion. September manipulated these events in giving Peter a choice between the two, and when he saw the future, he chose his own destruction - instead of the destruction of anything else.

7. September also takes Peter on a chase, where he is cornered by Peter on the rooftop. At the end of the episode we see: September and December watching the Bishops, revealing the reason behind all of the events of that day - and that is to know if Walter was really ready to let his son go. This almost leads me to wonder if December was also on September's side..

8. Fast forward to season 4 - we now see that September is in full universe manipulating mode. The Observers, unknowing that September is actually a mole - give him the device to erase Peter from existence. September does NOT erase Peter - causing him to be a target of the Observers for the rest of the season.

9. September manipulates Olivia mid-season by telling her she must die. September then shows Peter the "truth" about the Observers, and then also sends Peter on a wild goose chase into September's apartment.

10. The events that transpire are all in succession, but here's the big thing.. Bell knew the Observer watching the Bishops would be September.. not any other Observer, but specifically September. Bell has tech that should have NEVER been available to him before then.. Why September, and why a gun he can not dodge.. only one group of people wanted September gone at this point - the other Observers.

11. September shows up, creates a plan to bring an end to the Observers once and for all - takes out his tech? and figures out a way to feel again, all the while being human again as well. This involves a child, from the future, whom he has been watching since episode 11, of season 1.

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Everything has had a purpose.. everything. We weren't really having "Observer sightings" we were having September sightings, most of the events for the last 4 seasons were more than likely events the Observers were ok with - but they were all a part of September's plan, that's why we never really saw a whole lot of "other" Observer activity around our Fringe team.. only September.