This episode's glyphs spell:
The Observer is featured in this episode.
The name of the rail system in 'Marionette' is "Firefly Railway", foreshadowing the title and theme of 'The Firefly'.
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.
The Observer was orchestrating a plan to test Walter. At the end of the episode he discussed the event with December.
In '6:02 AM EST', as Walter struggled with the idea of allowing Peter to enter The Machine, he recalled the words of the Observer.
Walter accepted Peter's destiny in "The Last Sam Weiss" and watched as Peter stepped into The Machine and activated it. (Image 1)
Walter hypnotized Roscoe Joyce in "The Firefly". (Image 1)
In "The Boy Must Live" the Observer revealed that Michael was his son and that his observations of Walter and Peter affected his feelings about his own son.