This episode revolves around a thousands-year-old viral hemorrhagic fever that infects and then influences its victims to attempt to spread the viral particles outside of the building. Isolated inside with the rest of the exposed office employees, Peter and Olivia face life-threatening circumstances sending Walter, Broyles and Astrid on a frantic search for a solution to save them.
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Peter and others affected by the virus tried to burst through the windows of the office building to escape and infect others.
The Observer can be seen walking behind the CDC Field Director as he is talking with his assistant.
The storage box marked "Magellan Files" near Walter's library hiding place in 'Johari Window' foreshadows Walter's recollection of the Magellan's travels and the potential for decimation/extinction exploration can bring in 'What Lies Below'.
A courier in 'What Lies Below' carries a backpack that bears the logo of the "World Tolerance Initiative", foreshadowing Hoffman's planned attack at their 2010 Boston conference in 'The Bishop Revival'.
Walter opened a door to another universe in "Peter" and the world has been paying ever since.
Walter's Peter died in "Peter".