This mysterious man has been involved in the affairs of the X-Files since the day Section Chief Scott Blevins assigned Dana Scully to "assist" Fox Mulder. His silent presence in Skinner's office is always a warning that the government are keeping an eye on Agent Mulder. When not in Skinner's office, he can be found in the basement of the Pentagon, secreting evidence in a vast storehouse of classified materials. The tension between Mulder and The Cigarette-Smoking Man has increased steadily as the nameless man with the pack of Morleys increasingly involves himself in Mulder's work. 

In "Anasazi", we learned that his involvement goes back to the beginning, all the way to Fox Mulder's father. He may even be responsible for Bill Mulder's murder!  Many questions are raised in file 11: Patient X.  I won't say anymore, as there may be some fans out there who have not seen file 11, but those who have, will understand what I mean.