In this episode, Peter is taken back to the "Other Side" by his real father, dubbed "Walternate". FBI agent Olivia Dunham and Walter lead a team of former Cortexiphan test subjects to retrieve him after discovering that Peter is an unwitting part of Walternate's plans to bring about the destruction of our universe using an ancient doomsday device.
This episode's glyphs spell:
The Observer provided Olivia with a schematic of a machine, and Walternate was shown to have mostly built it in the Redverse. This suggests Walternate may want to use it for his cause.
The Observer can be seen dropping off a paper for Olivia at the bar.
Peter finds a bubble gum wrapper with a comic that says "You can't get there from here" in 'Northwest Passage', foreshadowing his visit to the alternate universe in 'Over There (Part 1)'
The two sides of the war, the Blueverse and the Redverse, become apparent in "Over There (Part 1)".
In "Over There (Part 1)" we see the amber quarantine protocol in effect.
As Olivia continued to regain her memories in "A Better Human Being" she mentioned remembering the events of "Over There (Part 1)".
Lincoln recognized Nick Lane when they saw each other in "Over There (Part 1)".