The vaccine was part of the Project created by the Syndicate to combat the alien virus known as Purity, also known as the black oil. Although the Syndicate was working with the alien colonists toward their colonization of Earth, the Syndicate saw to their own survival first and foremost. While simultaneously developing an alien/human hybrid for use as a slave race, the Syndicate also worked on a vaccine that would resist the black oil and ultimately destroy the alien race.

An early name of the vaccine was Purity Control. ("The Erlenmeyer Flask")

When Fox Mulder and Alex Krycek traveled to Tunguska, Russia, they learned that the Russians had developed a successful vaccine whereas the Syndicate had yet to do so. Both Mulder and Krycek were infected with Purity and healed by the vaccine. Krycek returned to the United States with the vaccine and helped the Syndicate by testing it on Marita Covarrubias.

When Dana Scully was captured and brought to Antarctica, the Well-Manicured Man revealed the history of the vaccine development to Mulder moments before his death. He provided a vial to Mulder, which he used to save Scully's life. (The X-Files Movie)

In 2001, following the reappearance of Mulder after his abduction, the existence of the vaccine came back into discussion. Without the healing provided by Jeremiah Smith, as Theresa Hoese had experienced, Billy Miles was completely transformed into a supersoldier following his abduction experience. Scully and Skinner were horrified that the same fate would befall Mulder if they were unable to stop the transformation. However, Skinner was approached by Alex Krycek, who had obtained a vial of the vaccine. The vaccine would save Mulder's life and keep him from becoming an alien replicate as Billy Miles had become. Krycek promised to provide Skinner the vial if he agreed to keep Scully's baby from coming to term. Appalled, Skinner chose instead to send John Doggett to forcibly retrieve the vial from Krycek. In their first encounter, Doggett faced off with Krycek but Krycek merely allowed the vial to fall from his hand and shatter on the ground. Resigned to defeat, Skinner thought it best to save Scully's child and pulled the plug on Mulder's life support equipment. Remarkably, in doing so, he halted the advanced of the virus and saved Mulder's life even without the vaccine. ("DeadAlive")

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