"Purity Control" refers to the codename of the project in which experiments are performed with the human/alien DNA. These experiments seek to create a human/alien hybrid, thereby creating an army immune to genetic warfare. It remains unsure, however, whether these experiments are known by the shapeshifter race (who are in league with the government) as they are clearly against human/alien DNA (See "Colony"), and aim to preserve the purity of the shapeshifter race.

• We are first introduced to the project codenamed "Purity Control" in Season One's final episode, "The Erlenmeyer Flask". According to "Deep Throat" the alien DNA is being held at the Fort Marlene High Containment Facility. Since the shapeshifters would get pretty angry if they found out their DNA was being mixed with that of humans it is probably safe to assume that the conspiracy is performing the tests for "Purity Control" in secret, and that the name "Purity Control" is an ironic joke. Or Dr Berube could have been part of "Purity Control" (which wants to prevent the alien DNA from being mixed) and rebelled with the flask and experimented on the shapeshifter blood for his own reasons.

• The next time we hear of operation "Purity Control" is in "Red Museum". Here the conspiracy rebels pay the local doctor to inject specific children with regular doses of alien genetic material. Perhaps here the conspiracy find out about this experimentation and object to it so they send Crew Cut Man to deal with it. Here more information has been found about the mixing of alien and human DNA that it renders the subject immune to disease (a step closer to creating the human/alien hybrid immune to genetic warfare).

• Possibly the next event related to "Purity Control" would be the events that look place in "Nisei/731". The NSA man tells Mulder that the "leper" in the boxcar is suffering from haemorrhagic fever, although it remains clear that the "leper" is a test subject, a soldier prototype immune to radiation poisoning and biological warfare. However haemorrhagic fever is a blood transmitted disease so is the conspiracy trying to make human blood have the same qualities of the shapeshifter blood (which is shown to be very deadly)? So if the conspiracy is creating these 'super soldiers' are they preparing for a war? To battle the grey aliens or conquer the world? The death of Japanese scientists and ''leper" victims are because the shapeshifter race ordered these killings because they want the purity of their race to be maintained, so the killings are the result of "Purity Control".

• Purity Control is also testing on Emily and Emily seems to be a valuable asset to the operation (perhaps Emily is very close to being the ultimate soldier immune to biological warfare etc) as the shapeshifters, working for the conspiracy (I think we can now safely assume that the shapeshifters don't have a problem with mixing DNA and that Purity Control's role is to create a alien/human hybrid), try to keep her alive by injecting her with greenish fluid. As Mulder says: Emily "was born to...serve an agenda". The tests on Emily are run by Dr Calderon who works for the Prangren company, however this man is quickly executed by the shapeshifters for stuffing up and in case he reveals anything about their plans. Any success attained with Emily diminishes as Scully lets her die so the project can not be furthered.

In summary, "Purity Control" is quite possibly a control body created by the conspiracy to monitor any experimentation with shapeshifter DNA and to prevent it. Dr Berube was a rebel scientist who took some of the alien DNA and experimented it upon human subjects, hoping to create the ultimate soldier and to possibly sell his 'weapon' to another country. These experiments continued in "Red Museum" using thechurch of the Red Museum as a control group. The conspiracy, while monitoring Mulder and Scully's investigations, found out about it and sent the Crew Cut Man to 'punish' the people involved in the testing and wiping out evidence of alien life in the process. Again Nisei/731 had the same scenario which resulted in the deaths of the scientists and the victims. As long as the shapeshifters are strict about the purity of their race "Purity Control" will remain operational.