In the first season episode "The Erlenmeyer Flask", Mulder and Scully come across an orange substance labelled "Purity Control". After having it analyzed, they learn that it contains alien genetic material. From the context of this episode, it seems to have some role in the human/alien hybrid experiments. It turns up later in "Red Museum", where it was apparently being injected into people (and animals) as part of some experiment. The wiki entry for Purity Control seems to indicate that its purpose was specifically to "create alien/human hybrids". This hybridization program was apparently an agreement made between a secret government syndicate and the aliens so that humanity would survive their eventual colonization, albeit as slaves.
However, in later episodes, it seems that the mass hybridization program, as planned, would be carried out infecting everyone with an alien virus (the black oil) carried by bees. We also learn that some of the members of the government syndicate were secretly attempting to develop a vaccine to resist the alien virus and stop the colonization. Every time that we see this vaccine, it is an orange liquid that looks exactly like Purity Control.
To complicate things further, we learn (years later) that the black oil/alien virus is actually called "Purity". Now whether this was a neat bit of foresight or just retconning is something that only the writers know. :)
So I guess I'm confused. The name "Purity Control" would indicate that it is a vaccine, but in the early episodes, it seems to be the agent by which the hybridization and colonization would be carried out.
Does anyone recall an episode where this was addressed?