Understanding Fringe requires an understanding of quantum physics. I'm not sure if the writers realize that.
The over-arching plot of the show is that Walter crossed into an alternate universe that closely resembled our own and now they are at war with us. The amount of suspension-of-disbelief that this requires is staggering.
First, the presence of alternate universes is dependent on the many worlds interpretation of quantum mechanics. There is no evidence that this is an incorrect interpretation. But it is unsatisfying and not generally accepted. The generally accepted interpretation is the Copenhagen Interpretation. There is no evidence that the latter interpretation is the objective reality...mostly because the later interpretation denies the existence of an objective reality, but still.
The difference between the two views can be illustrated simply with Schroedinger's Cat. Imagine a cat placed into a box with a poison vial that will release the poison as soon as a radioactive decay occurs. The Copenhagen interpretation: Since, for a radioactive decay to occur, the waveform of the nucleus needs to collapse, and only an observation can collapse a wave function, as long as the box is closed the cat exists in an indeterminate state; it is both alive and dead at the same time. The many worlds interpretation: the wave form collapses at every time that is probabilistically possible. Each possibility creates another universe. In some universes the cat is alive, in others it is dead.
Though at first blush the Copenhagen interpretation seems deeply unsatisfying it passes the Occam's Razor test: it is the simplest explanation that fits the facts. The more I learn about quantum mechanics, the more I like that. I find the many worlds interpretation appalling. Consider radioactive decay as an example. The decay of a radioactive isotope has a finite probability of occurring at any moment. At every moment it can decay, and in this interpretation it does and in doing so it creates a new universe. Time, though uncertain, is not quantized like energy is. That means that, just in observing the decay of one atom over one second, and infinite number of universes have been created. There are about 10^80 atoms in the universe, and each one results in the creation of an infinite number of new universes every second. That means that every second, 10^80*infinity new universes are created. Can you see now why this feels a little absurd?
But if we assume that the many worlds interpretation is correct, what are the chances that we would find a parallel universe like that which is depicted in Fringe? I'll cover that next time.