He's Not Dead
Alright, I'm going to take a crack at it:
The whole thing that happened with the Blue-verse and Amber-verse is not that Blue-verse no longer exists or that it does exist and Peter has to find a way back to it. Blue -verse is Amber-verse! Amber-verse is Blue-verse! And how, because of a little esoteric practice called alchemy.
I also believe that Olivia's headaches are caused from her crossing over to the Blue-verse. But she only does so when she's sleeping... As in she doesn't actually go back to Blue-verse, but she subconsciously remembers being there. And her headaches arrive in the morning when her brain has to deal with the schitzophrenic shock of not only being back in the Amber-verse, but also in realizing that the Blue-verse she was dreaming of in such vivid clarity completely doesn't exist.
This is where Nina Sharp comes in and her involvement could run one of two ways. Either she is injecting Olivia at night with the Cortexiphan to stop her dreams about the Blue-verse and Peter. Or she is injecting Olivia to cause the dreams.
We recall that Olivia had previously only had headaches when she crossed universes and it stands to reason that they wouldn't throw in that factor just as a Red Herring. Hence, one could conclude that, per say, one does not need to REALLY enter another universe to experience it. Perhaps in Olivia's case, one only needs to dream it to have experienced it and thus received the headaches from a simulated dream transferral.
But going back to Nina, I want to guess that she is the one causing Olivia to have the dreams mostly because, as others here have noticed, she seems very interested in Peter and Olivia's other-dimensional-relationship with him.
But why all this fuss over getting Olivia to remember the Blue-verse and Peter? (if that is the case)
It's because this has to be some kind of alchemical work. Peter's deletion was the primary cause of the Blue-verse's shift into Amber. And in the Amber-verse Olivia was previously the closest person to Peter, and hence the Blue-verse. She is a kind of fulcrum point. If Nina can get Olivia to snap out of the Amber-verse mindset and back into the Blue, then Olivia's actions once she wakes up will probably cause some kind of ripple effect within the Amber-verse. And with enough ripple changes, maybe the Amber-verse will revert back to Blue.
But then again, why would anyone want this to happen? Why would Nina?
I mean, technically speaking, there's nothing wrong with the Amber-verse. The only thing wrong in it is Peter, and a few people having funky dreams about stuff that didn't happen. So why try to bring it back? Perhaps, once the Bridge-verse was created between season 3 and 4, wasn't it curious that the show skipped that entire scene of the two universes staring each other down. We know that a taudry peace has been struck between the universes as evidenced in the first episode of Season 4. Hence, in that Bridge room, was a deal struck? And perhaps was that deal that the Blue-verse be alchemically altered into the Amber-verse? (and perhaps even that Peter get taken out of the equation?) Perhaps the Blue-verse was becoming too powerful with Massive Dynamic at its side. And what if some higher ups in the Blue-verse don't like that deal? I'm just saying...as far as things have worked out, Massive Dynamic has actually lost on the deal.
Massive Dynamic does not have Bell as its head scientist, and though Walter is functional, he is a shadow of the genius he had become in the Blue-verse. Given these things, I darn well bet Massive Dynamic, and hence Nina Sharp herself would love for things to return to how they were. Hence her fiendish thief-in-the-nightery.
I also believe that it was never the intention of the Observers to knock Peter out completely. It was just the basic fact he had a dimension altering Deus Ex Machina under his own control that gave them pause for concern. Basically with his erasure and re-introduction, they were telling Peter to slow his roll a bit. The Observers want peace for both universes as well, but the way things were going in the Bridge-verse, Blue-verse was bringing the unlit matches, Red-verse was bringing a gallon of oil, they were trying to make a deal, and then stumbles in Peter with a lit cigarette! So yeah, my gut tells me this Amber-verse thing is all part of the plan.
But so who are these new shape shifters then? Well, break out the ole Ockam's Razor (spelling?) and I'd have to guess that they are spies from the Red-verse to make sure Amber-verse is playing by the rules. Or they're soldiers from that ZFT outfit who just want to see the Apocalypse happen for the LULz.
Alright, that's all I've got for now.
I've always explained the looping and rewriting nature of the timeline in the blueverse to be that of a tape recording over itself repeatedly. The Amberverse is just the most recent, "top" layer of the rewrite.
I'm starting to think we can explain a ton of things by saying that the previous layer is still buried underneath somewhere - just not accessible.
Since Season 1, Fringe has always had a strong connection to dreaming and dream-states, and to drugs. Bell and Walter originally became obsessed with the alternate universe idea after experiencing it while on drugs like LSD.
I think we can combine a great number of things under this premise.
- I don't remember what episode, i'll edit this later, but the one where Peter has the stray memory of Walter's in his head and doesn't even know it?
- Olivia's first version of the "Redverse" in S1, only with paper, cortexiphan trials, and the FBI
- Bell having seen history repeat itself many times - I'm sure he (and his soul magnets) have uncovered many layers of William Bell's experiences inside Bell's head, especially with his experimentation with drugs.
- portions of the episode LSD
- Olivia's dreams
- A solution to this whole Peter going home/S1-S3 reboot complaint.
I also have a theory on the origin of the machine/loop.
The machine was built in an original timeline where some combination of the Walters, Bell and Peter built the machine. We know nothing about this timeline for sure, but we know that for some reason, Peter was *significant.*
Things start off in a timeline where Blue Peter dies, and Red Peter is cured, and lives. Walter and Bell still experiment with alternate universes, sending the car and what not. After Peter's death, Walter gets very into his work, becomes very obsessive; He never has a kidnapping plot, although the thought of seeing Peter may still motivate him. He ends up building the door and crossing over. I think that in the original timeline, with Peter being a voice of reason, there is no war. Instead, Blue-Walter and Bell are recognized as the scientists they are; the damage accidental; They may actually be allies by the time the damage becomes known, who knows? With Walternate having no reasons to hate or distrust; His brilliant son Peter at his side, it would all be seen as an amazing scientific marvel. With no kidnapping or death to start the conflict, the damage to the red-verse is solely accidental, the results of experimentation gone wrong (as they were attempting to cross over for the sake of science, well before Peter's illness). With no harsh feelings, the two sides team up to save the Universes. In the process, Red-Peter (the significant one that was being observed) meets Blue-Olivia, they become the Machine's operators (and their bond begins), and by working together the two sides build the machine to save the Universe. Unfortunately, the damage is too late, the wormhole forms, and the machine is sent back, with clues left, hoping that by discovering the machine in our time rather than building it in our future, they can save the world before the damage is irreparable. This next cycle should have worked, but thats when September interfered and threw everything off.
It really doesn't matter which Universe it was built in, either. How did the Machine get into both Universes?
Alternate Universes are made when you make different decisions... when things could turn out differently, branching further and further as you go, into infinite possibility.
The wormhole in central park is in the blue universe, and it is the blue machine that is sent back in the loop. That doesn't mean that it wasn't originally built in the red-verse, by the Significant Peter that was being Observed in the red-verse pre-series, pre-loop.
The wormhole sends the machine (origin: either universe, but i assume red for the *original* creation, blue for all subsequent send-backs) back to 250,000,000 years ago. This is before there are humans; before intelligence has developed on the earth - before *decision making* begins branching infinite possibilites of possible human actions. The machine, then, presumably, ends up in the shared history of all Universes. It was only built once and that was covered up by countless rewrites.