This episode, "Neither Here Nor There," mirrors the very first episode of Fringe. We have an FBI agent named Lincoln Lee who has just lost his partner to some fringe science problem that turns his skin translucent, and this is exactly what happened to Olivia Dunham in the first episode. The alternate Olivia mentions how alone our dimension's Olivia is, and in fact, most of the characters feel more alone. It is even said that Walter has never had anything to tether him to the world, and as a result we see a mad scientist who isn't even allowed to view crime scenes except remotely through Astrid. Also, before "the change" Lincoln Lee and Olivia Dunham knew each other, but during this episode they met for the first time...
It's a different world(s) with different mysteries. So, let's just jump in.
1. The Bleed / The Man in the Mirror
In the beginning of the episode, a Pattern Observer mentions that though Peter Bishop was erased from continuity traces of him continue to bleed through. From the beginning of the episode, Walter and Astrid experience problems - a squawk - with their communication via blue tooth headsets. Perhaps this is just a way to introduce the fact that Walter is not allowed to go to the crime scenes, but I'm banking on the fact that Peter Bishop's presence is blocking these signals.
Later in the episode, Walter emerges from his Altered States sensory deprivation chamber terrified and ranting about hiding from The Man in the Mirror. We can be certain, at that point, that this is Peter Bishop bleeding through. But in case any of us didn't pick up on it, the last scene explains it plain and clear. Peter Bishop appears in Walter's television screen.
And let's not pretend that this is all we saw of The Man in the Mirror. Much as Tyler Durden appeared here and there, spliced as if into a film reel, in Fight Club, so also did Peter Bishop appear in this episode. Now, all I can speak of is one time. I saw a flash of Peter in the background of the scene where Walter and Astrid are talking about whether or not Walternate is evil. My assumption, however, is that I missed more appearances. Did you see any? Here's mine.
Remember how everyone was looking for The Pattern Observer in the background during season one. Well, now we're going to be looking for Peter Bishop. Yes. You heard it here first: The Bleed is the new Pattern Observer.
2. You Did This To Me!
All of the things that have happened so far are, in some way, connected to the actions of the Rogue Pattern Observer, the one who seems connected somehow to humankind, and in particular to the Bishop family. At the beginning of the episode, this Rogue Pattern Observer was charged with erasing Peter Bishop from existence completely and finally. His "boss" explains, "They can never know the boy lived to be a man."
For a few minutes there, I thought this was going to set the Rogue Pattern Observer and the Pattern Observers in general as the overarching enemies of this episode. And this may actually prove true over time. But in the end, the Pattern Observer cannot flip the switch and erase the adult Peter Bishop.
As a result, The Man in the Mirror, Peter Bishop, appears to Walter Bishop. And according to the Prologue discussion between the Pattern Observer it is safe to assume that this is our little speck of hope that adult Peter Bishop's existence will be known. But whether or not he is known of remembered, there still remains the task of fully integrating him back into reality. And the Pattern Observers don't seem to want that to happen.
3. It's Still Quite Dead
When Walter transforms an inanimate bird body into a flying bird, he is asked if he just resurrected a bird. Walter responds, "No, no. It's still quite dead." But later he mentions, "It's a start." It appears that while he may not have restored life, he restored motor functions for a limited time to a bird that was once dead.
It seems like Walter is hell-bent on learning the art of resurrection, and for good reason: two versions of his son died from an unexplained disease when he was young. Will Walter successfully learn how to resurrect a human being? What will the repercussions of bringing someone back from the dead be? Or will The Man in the Mirror convince Walter to let go of his son?
4. Biological-Chemical Hybrids
After two of the translucent villains from this episode's plot arc were shot and killed by Olivia and Lincoln, their bodies were autopsied. Walter finds out that they are biological-chemical hybrids, created using science that isn't available in this universe but which is certainly from the alternate universe.
Walter immediately assumes that these villains are the work of Walternate, but for some reason this screams of a Red Herring to me. I think that they are the work of someone else, perhaps a William Bell from the alternate universe who survived in a world without Peter Bishop. Perhaps someone else entirely. But then again, maybe Walternate is always a bad guy, kind of like Sloan on ALIAS.
5. References
Since this is a J.J. Abrams show, we know that there are going to be outside-references abounding, and this episode is no exception to this rule. I found five references. Maybe you found more:
(1) Walter points Lincoln Lee's attention to the ear that he is growing "under the dome," which is possibly a reference to the Stephen King novel Under the Dome where an unexplained dome appears over a city and all is turned to disorder inside.
(2) Walter later mentions that he read a book called The Spy Who Came in from the Cold while in the mental institution, a book by John le Carre that was made famous for pointing out the inconsistencies between Western espionage and Western democratic values.
(3) When the translucent villain peals his fingernail off, you can be sure that this is a reference to the 1986 Jeff Goldblum film The Fly, which details the terrible consequences of messing with advanced technology.
(4) Whenever Walter sees Peter Bishop in the corner of his eyes, he becomes frightened and begins to rant about The Man in the Mirror. This is no doubt a reference to the Michael Jackson song "Man in the Mirror," in which Michael Jackson teaches that the best way to change / save the world is to begin by looking in the mirror and changing who you are. You want a better world. Make yourself a better person.
(5) Finally, as I mentioned before, the appearances of Peter Bishop in the background mimicked the way that Tyler Durden was spliced into the film Fight Club at various points.
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