A highway construction worker in rural Pennsylvania goes missing when he is mysteriously drawn into an underground tunnel filled with human remains. Meanwhile, back in the lab, Walter is attempting to simulate travel between realities on frogs. When it's discovered that the disappearance in Pennsylvania is not an isolated incident, the Fringe team travels to the crime scene to unearth evidence.
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Certain events in this episode mirror the struggles Walter is going through in his personal life, such as the line "The grave of a boy... who was not in his grave", a reference to Walter visiting the grave of Peter Bishop in the season 1 finale. Alternatively, "mirror" could be a reference to the Shapeshifters in the previous episode who could mirror their look after anyone else.
The Observer stands in the field near the Hughes house just before Agent Jessup finds the bible.
The car crash in 'A New Day in the Old Town' happens in front of a business called "Gruno & Dunder", an anagram for "underground", foreshadowing the killer's location in 'Night of Desirable Objects'.
The two Canadian National locomotives in 'Night Of Desirable Objects' each bear the logo "CN". This foreshadowed the goal of "Project Tin Man" in 'Fracture', to combat the effects of Cyanogen, a nerve gas with a chemical formula of (CN)2, and alludes to the fact that the Cyanogen-related explosion occurred in a train station.
2, and alludes to the fact that the Cyanogen-related explosion occurred in a train station."
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Just like Peter, who doesn't know that he took the place of the real Blueverse Peter who died in "Peter".
This mirrors the struggle Walter went through in "Peter".
He suffered some of those consequences in "Over There (Part 2)".