The X-Files has many themes, but there’s always some kind of underlying story to be told. I believe this episode hints towards the greater picture, when a highly contagious infection starts spreading in a prison, and then out into the open. Mulder joins US marshals on a man hunt while Scully tries to figure out what’s been going on and how it spreads. The smoking man naturally makes an adherence in Skinners office when Mulder questions the reasons behind being assigned the case.
Though nothing is given away, a dying scientist confides in Scully, informing her that the US’s largest pharmaceutical company intentionally infected prisoners – then lost control and tried to cover it up. Mulder wants the public to know, but Scully isn’t too sure. Later on when it’s all brought under control, the pair go about trying to prove what they’ve witnessed, only to find the Smoking man and Skinner are unwilling to lend any support. Mulder gets some friendly advice from Skinner to watch his back, this is only the beginning.
Mulder still presses to find out where Skinners loyalty lies, although we know he reopened the X-Files to hurt the likes of the Smoking man, he still shows reluctance to help Mulder in anyway possible. Nothing X-Filey about this episode, or paranormal, just good old fashioned government cover ups!