Mulder: I found this in Agent Krycek's car. He doesn't smoke. Agent Krycek was the last person with Duane Barry before he died. He was also the last person to see the tram operator before he disappeared. When I got to the top of Skyland Mountain, I saw an unmarked helicopter working the area. I believe that Agent Krycek gave away the whereabouts of Duane Barry and Agent Scully to whoever he's working with.
Skinner: And who is that?
Mulder: I don't know, the military? Some covert organization within the government? Whoever it is that man who smokes those cigarettes works for.
Mulder: Because Agent Scully got too close to whatever it is they're trying to deny. Because she had hard and damning evidence, that metallic implant in her possession. Or because her termination would prevent further involvement with me and my work.