In this episode, Peter gains the trust of Olivia and Agent Lee and leads Lee to the alternate universe to try and find a path back to the timeline he knows. Meanwhile, the hybrid shapeshifters have a foothold in both universes and the man controlling them has infiltrators buried deep in Secretary Bishop's ranks.
This episode's glyphs spell:
The Observer is featured in this episode when he gives Olivia a dire warning in the opera house.
The ParkView Hospital logo in 'Wallflower' foreshadows the return of Walter's universe portal in 'Back to Where You've Never Been'.
When Peter and Lincoln cross to the Redverse in 'Back to Where You've Never Been' they walk by Mohonk Tea House, foreshadowing Mohonk Quarry that's central to David Robert Jones's plan in 'Enemy of My Enemy'.
This is how Peter killed David Robert Jones in "There's More Than One of Everything". (Image 1)
A double-decker car is visible in the Redverse in "Back to Where You've Never Been". (Image 1, 2)
She was right, and those events began in "Peter". This mirrors what Walter said in "Peter".
Olivia was upset in "Marionette" that Peter looked into Fauxlivia's eyes and couldn't tell that it wasn't Olivia.
In "Letters of Transit", which takes place chronologically in the future, Olivia isn't present; only Peter, Astrid, and Walter are featured.
Walter shot Olivia in the head in "Brave New World (Part 2)" in order to stop her being used as a power source for Bell's new world. (Image 1)