Fringe is one of my favorite TV shows, largely because of the moral and religious themes that appear in it. However, one of the basic premises of the show would seem to nullify morality itself.
The major plot arcs in Fringe concern an alternate universe, very similar to our own, but differing in some ways. Most people seem to have a doppelganger in the other universe, and their personalities are often different, sometimes extremely so. In one episode, a peaceful psychology professor on our side has a counterpart in the other world who is a serial killer. The parallel universes make for some great sci-fi storytelling but may be necessarily opposed to free-will.
In the show, Dr. Walter Bishop explains the concept of the multiverse, in which every possible outcome, including every possible decision made by an individual, is contained in a separate universe. If this is an accurate description, then the multiverse must be ruled by material determinism, and free will is an illusion. If every possible future occurs across an infinite number of universes, it can only be because each future is the result of material processes that differ somewhat in each universe. This is not problematic when one is just considering animals, vegetables, minerals, and star clusters, but when applied to people, it would seem that human action consists of nothing more than the predictable and material neurological response to purely material stimuli.
The Fringe writers are aware of this problem and sought to address it in one episode. FBI agent Lincoln Lee and his doppelganger were comparing their life histories while working on a case together. The two men have markedly different personalities but found that they grew up and matured in almost identical circumstances. Lee 1 asked Lee 2 how this could be, and Lee 2 said that he believed their differences are the result of free will. Could he be right?
For Lincoln to be right about free will, Walter must be wrong about the multiverse. If alternate universes are not an infinite collection of materially determined outcomes but are non-deterministic worlds in which free will exists, then a different problem presents itself, namely, probability. The two universes are not identical, but the similarities are so great as to be ridiculously improbable. For example, almost everyone in one universe has a counterpart in the other. Think about the family tree that precedes each person all the way back to the creation of man. For even one person to exist in both universes, every one of his ancestors in both worlds had to be conceived and themselves beget children successfully. One person might have a different number of relatives than their counterpart, but their direct line of ancestry would have to be exactly the same. One person existing in both universes is absurdly improbable and billions of more human pairs such as those in Fringe are even more improbable. An infinite number of materially determined universes solves the problem of probability, but does away with free will. However, there is one way that free will could exist in realistically probable parallel universes.
Two different universes could be very similar, contain versions of the same people, and include free will, if both "universal destinies" were guided by Divine Providence. By inspiring good and allowing evil the same way in both universes, God could guide humanity's development towards a similar future. This might sound like a heavy handed, Calvinist God, but I don't think so. The genealogy of Jesus was divinely guided, but His human ancestors had free will. The Crucifixion was predestined but Christ's executioners had free will. Why would Jesus ask his Father to forgive them unless they had freedom, and thus moral responsibility for His death? Similarly, God might guide the universes and their occupants to a particular destiny. This sort of divinely inspired parallel universe scenario may be a bit of a stretch, but I think that it is the most satisfactory way to reconcile free will with Fringe.