This episode follows a series of organ recipients being tracked down and having their donated organs removed all in a scientist's attempt to resurrect his deceased love interest whose organs were donated to the victims. Meanwhile, Olivia copes with the consequences of being back in the prime universe.
This episode's glyphs spell:
After seeing the extent to which Fauxlivia infiltrated her life while she was away, Olivia struggled to adapt to her new circumstances.
The Observer can be seen across from the Malt Shop that Walter and Peter go to for milkshakes.
The electronic billboard outside Springsteen Station in 'Entrada' displays advertising for "Mercy Ballet", foreshadowing the victim of 'Marionette' being strung up like a puppet and made to dance like a ballerina.
The name of the rail system in 'Marionette' is "Firefly Railway", foreshadowing the title and theme of 'The Firefly'.
Olivia was upset in "Marionette" that Peter looked into Fauxlivia's eyes and couldn't tell that it wasn't Olivia.