In this episode, Olivia is forced to recount her time spent as a child in tests conducted by Walter to regain the ability to see objects that have been influenced by the parallel universe and prevent the deaths of innocents. Olivia comes to learn the truth about Peter, that he is from the parallel universe.
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The truth about Peter was finally revealed to Olivia at the end of this episode when she saw him glimmering.
The Observer can be seen in front of a fire truck when the Fringe team arrives in New York City.
A poster in the alley where Hoffman tests his weapon's toxin dispersal in 'The Bishop Revival' says "The Glimmer Brothers", foreshadowing Olivia recognizing objects from the alternate universe because of their glimmering nature in 'Jacksonville'.
A police barricade in 'Jacksonville' says "DO NOT CROSS", foreshadowing the conflict between Nina, Carla, and Walter as Nina and Carla try to stop Walter from crossing universes in 'Peter'.
Rebecca noticed the same glow about Peter as Olivia did in "Jacksonville".
This is exactly what Peter's biological parents experienced in "Peter".
The combination to Bell's safe in "Concentrate and Ask Again" was 0-5-2-0-1-0. This was the combination Walter used to access the daycare center in "Jacksonville".
Nina found a toy Monte Carlo in Bell's safe in "Concentrate and Ask Again". (Image 1)
A double-decker car is visible in the Redverse in "Back to Where You've Never Been". (Image 1, 2)
As Olivia continued to regain her memories in "A Better Human Being" she mentioned remembering the events of "Jacksonville".
The combination to access Bell's safe in "Five-Twenty-Ten" was 0-5-2-0-1-0, the same combination Walter used to access the daycare center.