When the Fringe team visits Massive Dynamic's assembly of the doomsday device Walter becomes greatly concerned for Peter's well-being, so he turns to Nina for added brain power to understand the relationship between Peter and the superweapon. Meanwhile, the discovery of a dead shapeshifter body triggers an intense investigation.
This episode's glyphs spell:
Walter theorized that Peter's proximity to The Machine, an object of destruction, altered Peter to be similarly dangerous and destructive.
The Observer can be seen in the crowd near the crime scene at the koi pond.
The album cover artwork from The Police's 1981 album Ghost in the Machine can be seen painted on a wall in 'The Firefly'. This foreshadows 'Reciprocity' where The Machine seemingly turns on for no reason.
A blue recycle bin in 'Reciprocity' in the alleyway where Peter kills a fleeing shapeshifter is labeled with a "Powder Blue" sticker, foreshadowing the blue powder bioweapon used in 'Concentrate and Ask Again'.