This episode follows Nazi scientist Alfred Hoffman as he specially designed airborne toxins to kill only surrounding people with similar genetic traits, such as people with brown eyes. Adding to the intense lab investigation, Walter uncovers an alarming formula that reveals a link to a branch on the Bishop family tree.
This episode's glyphs spell:
Walter's father was involved in the creation of the toxin used in this episode, and the villain was his contemporary.
The Observer can be seen walking outside the cafe when Alfred Hoffman is talking to the mother and daughter inside.
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'.
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'.
In "Peter" he literally crossed universes for family.