The Syndicate uses a pharmaceutical company to test the spreading of a lethal contagious disease by triggering an outbreak in a prison. M&S unwillingly become part of the Syndicate's plan when they help hunt down 2 escaped prisoners.
F. emasculata and its parasite
Tools of the Syndicate
Using the manpower and research of Pinck Pharmaceuticals, itself passing as the CDC (governmental agency Center for Disease Control), the Syndicate tests in the open how a fast virus spreads. This profile resembles very much 4X21: Zero Sum; when the colonization begins, the Purity virus will be released through bees. At this time this last detail hasn't been decided yet, and the Syndicate still looks for the best way a virus spreads. The Faciphaga emasculata and its parasitoid are the best vector around, so much that it warrants a test.
But Pinck Pharmaceuticals isn't entierly clean on this either. They are fully cooperative with the Syndicate on this outbreak, and this is the kind of thing that the company does in secret (Dr. Osbourne: "Don't believe for a second that this is an isolated incident.") Mulder thinks it's a way "to circumvent years of F.D.A. trials in order to get their drug on the market." Thus Pinck Pharmaceuticals has something to gain from all this, the National Guard is just following orders and the FBI can't blame anyone but the Post for making a mistake that never was one.
CSM: "It's done every day."
Elizabeth: "If that's true, how come it's not on TV? How come they're not telling everybody?"
Mulder: "That's not my decision."
Elizabeth: "Well, whose decision is it? You knew about it and you didn't say anything! Why should I tell the truth if you won't?"
Dr. Osbourne: "Don't believe for a second that this is an isolated incident."
Skinner: "For every step you take, they're three steps ahead."
Mulder: "Well, what about you, where do you stand?"
Skinner: "I stand right on the line that you keep crossing. I'm saying this as a friend. Watch your back. This is just the beginning."