Major Season 4 Spoilers ahead but it's impossible to ask this question without them:
Every indication we have so far is that the Observers are from our universe. We learn that they are
us, in the far distant future,
and I assumed that meant they were from the same universe as the main Fringe universe, as opposed to some alternate one. They focus much of their attention on our universe and the timeline of events here, and we eventually learn that they
come back to our time and conquer Earth, after destroying it in their time.
However, the explanation story we get for why September was so interested in Walter and Peter's lives has a major loophole. Specifically:
September tells Peter that, in the original timeline, Peter was "important", but he (September) screwed things up by distracting Walternate from curing his illness. He further mucked things up by saving alternate Peter's life, thus allowing him to impregnate Fauxlivia. Their child, Henry, did some unspecified thing that ruined the future for the Observers. To undo this mess, the Observers designed the machine, and arranged for Peter to have it built. The machine un-saved Peter, rolling back everything that happened to him as an adult, preventing the child from being born to Fauxlivia.
But in our original universe, before any interference from anyone, Peter died. It is Alternate Peter that would have lived. Does that mean that the Observers are actually from the alternate universe, and are only interested in ours because of what Walter did?
Are over-here's Peter and Olivia allowed to have a baby (which they clearly do, Henrietta) without screwing up the future? Or is what 'Etta is doing in our near future the thing that over-there-Henry did to screw up the Observer's future? How can events in our universe affect the future of the prime universe, especially if they are no longer connected?