I think I’ve been waiting for an explanation of the “Observers” for quite some time. I was blown away by the last scene where both Olivia AND Nina Sharp are being held captive.
We started out with the "real" universe and the "Walternate" universe, where Walternate was the "bad guy." We're now in a "prime" universe pair (where Peter didn't survive at all), and as we saw, in the "Walternate Prime" universe, Walternate is a good guy, while the chief scientist for the government/Massive Dynamics was one of the "new" shape shifters. I think that Nina Sharp in the "Walternate Prime" universe is behind the evil, and she crossed over secretly and has been working to unite all the different Olivias for some nefarious reason.
Mark