The Smoking Man
Six weeks later a mass contagion, the Spartan Virus, begins to break out, causing people's immune systems to break down; all but those with alien DNA in their system. This is part of a scheme by The Smoking Man, something which has been put into motion since 2012 (the year the supposed alien invasion was meant to take place). Scully works to try and find a cure by using her alien DNA and Mulder disappears and confronts the Smoking Man in an attempt to stop his plans. Scully finds out that The Smoking Man enlisted former FBI agent Monica Reyes as an assistant to his schemes.