In this episode, Walter sets out on his own after uncovering another tape and steps into a pocket universe sandwiched in the membrane between parallel universes. Observers converge on Walter's position and only Peter has the skillset needed to rescue the science team.
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Half of this episode takes place in a pocket universe, a split in the membrane that separates the two universes. Peter and Olivia are also starting to diverge from each other after Peter absorbed the Observer tech.
Observers are featured in this episode.
Graffiti behind Anil's van in 'An Origin Story' says "Ask Alice", foreshadowing the theme and title of 'Through the Looking Glass and what Walter Found There'.
The bell-shaped lamp in the pocket universe in 'Through the Looking-Glass and What Walter Found There' foreshadows the team gaining access to William Bell's storage facility in 'Five-Twenty-Ten'.
September told the team how Michael was a naturally more advanced human. In "Through the Looking-Glass and What Walter Found There" Michael had been hidden in a pocket universe accessible from room 413 of an apartment building. Episode S4E13 of Fringe is entitled "A Better Human Being." (Image 1)