This episode centers on three mental patients who mysteriously became sane again after shapeshifters from the parallel universe removed a piece of foreign tissue from each of their brains. This tissue is later revealed to have been taken from the brain of Walter Bishop years before. The fringe team of Olivia Dunham, Peter Bishop, and Walter investigate and face a new enemy, Thomas Jerome Newton, whose purpose is to decipher the missing parts of Walter's brain and find out how to move between universes.
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This episode's glyphs spell:
Thomas Newton's goal was to get Walter to remember details about his portal between universes.
The glyphs from S2E08 - August refer to this episode and are now safe to read for those who have been avoiding spoilers.
The Observer can be seen across the street as Olivia, Peter, and other FBI units go down to the men's restroom looking for Walter.
Signage in Chinatown in 'Snakehead' says "Ginseng Improves Memory!", foreshadowing the plot of 'Grey Matters' where pieces of Walter's brain are recovered to help restore his memories.
Colorful butterfly drawings hung up at Dunwich Mental Hospital in 'Grey Matters' foreshadow Walter's discovery of Edina's permutation secret in 'Johari Window' when he captured a butterfly for Astrid that later seemed to change its appearance.
Newton was referring to the events of "Peter" where Walter's Peter died and Walter crossed universes to kidnap another Peter.
Similar phenomena started happening in "6:02 AM EST". (Image 1)
William Bell removed pieces of Walter's brain at Walter's request as seen in flashbacks in "Grey Matters".
In "Transilience Thought Unifier Model-11" Walter's brain was partitioned to keep Observers from reading his mind and learning his plan to combat them.