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Originally Posted by octothorp
I think Walternate being Mr Secretary is the most likely thing, but I'm sort of hoping they throw another loop in there - something we haven't thought of. I also think their motives have more to do with William Bell and Massive Dynamic stealing technology from the other universe than about the theft of Peter. Or perhaps the blight is somehow the fault of our universe.
Also, the previous episode, with the time-traveller trying to go back to save his girlfriend was revealing: I thought that the Fringe universe would have an approach to time travel similar to, say, the recent Star Trek movie: that going back in time actually creates an alternate reality. But in that episode, we saw someone basically rewinding a single timeline, more like Back to the Future. Which casts doubt on my theory that it would be someone from our time travelling back to the past that causes the initial break between the two realities.
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There are theories circulating that the "blight" is what Walternate would have ended up curing if he had been the one to discover the cure to Peter's illness. That would also possibly explain how Peter is "significant". And there's also a lot of ambiguity as to whether it was "our" Peter who is significant, or only Alt!Peter.