Upon reading the Trivia for this episode, it is shown that there are several remarkable X-Files parallels here. Season 2 was rife with them.
A bike messenger and a Bald Non-Observer man, both enter "Vitas Petroleum," which in itself is an ironic name for the Oil company - Vitas, based on the Latin "Vita" is a Lithuanian name - MY name, meaning "Life." This tickled me, but it also has relevance to the episode at hand. The bald man in fact brings a deadly contagion into the Office.
Meanwhile, Walter is lecturing some children in a Museum - At first it appears that he is doing this with the grace of the institution, but in fact he just walked up and started telling the kids some scary facts about early world exploration. His delivery in this shows that Walter, our Walter, loves children and he was enjoying himself immensely as his mind is childlike in itself: and the kids were not that bothered by his stories. But a Museum Pencil Pusher/Bean-Counter takes offense to Walter's ad hoc teaching methods and they revoke his membership. It is also important to remember what he was talking about: Out of the large crew of Magellan's ship, very few of them made it back home, and in fact it was those survivors that brought back life saving information for the European World.
This episode has two X-Files regulars, Megan Leitch as Elaine, who played Fox Mulder's grown up "Sister" Samantha and Brendan Beiser who was "Agent Pendrell" in several X-Files.
And in fact, this episode deals with Oil, which in The X-Files was a delivery system for an alien intelligence. In this Fringe MOTW Episode the Oil is a delivery system for an intelligent virus. Also, the core sample which the Bald Man Vandenkamp (Nicolas Von Zill) left in his rental car is from an ancient geological era, which was a story element used in at least 2 X- Files, season 1's "Ice" and Season 4's "Gethsemane" - Both which had ice-core samples in which a life form was trapped. So this could in fact be the same X-Files "Black Oil".
Those infected with this permutation of "The Black Oil" have a burning desire to exit the building and breathe on someone - So they can infect more people. This rapidly becomes an untenable situation and to make matters worse, Olivia and Peter become trapped in the building under CDC quarantine.
Walter cannot allow Peter to "Die Again" - Astrid asks him what he means, we as viewers know about Peter's grave, but Walter has not yet told everyone, he fears the consequences. In most of Season 2, Walter holds tightly to this "secret" and the depiction of Walter grieving over telling Peter this fact is one of the better character developments of Walter.
Walter is in fact a year and a half out of St Claire's: That innocence of his that so defined him in Season 1 gives way to his internal conflicts of seasons 2 and 3. It is almost cruel to expect him to have to deal with this so soon after being brought back into the world, and this is just one step for him in his struggle to finally deal with the realities of what he ultimately is responsible for: Shattering two universes.
Walter is not a man who shirks his responsibilities, and that is shown here in the way he puts himself at risk for Peter and Olivia.
Walter's remarkable mind finds a way to defeat this insidiously clever contagion, but can the cure be delivered in time to save all of the people in Vitas Petroleum? Olivia knows a way but she has to deal with an obstacle she does not expect: Peter.
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