 Shortly after Skinner arrives home he is met by Mulder , who tells him about the case and the fact that someone is going to great lengths to cover it up . Mulder reveals that Detective Thomas was killed , which shocks Skinner . Mulder tells Skinner that Scully is undergoing tests regarding her cancer . Later that night Skinner meets with The Smoking Man , who is accompanied by Thomas ' murderer , the Gray Haired Man ( Morris Panych ) . Skinner is angry that Thomas was killed and wants to end their arrangement , which The Smoking Man refuses to allow . Mulder calls Skinner , telling him about the woman 's body being burned and the blood evidence being tampered with . Mulder tells Skinner that he is trying to match the bullet that killed Thomas to a gun issued to a federal agent or local officer . Skinner searches his drawer and realizes that his gun was missing and must have been the one used for the murder . Skinner , realizing he has been set up , calls The Smoking Man , who confirms that Thomas was killed with Skinner 's gun and that by going to the police Skinner would end up implicating himself in the murder . The Smoking Man refuses to provide any details on what he is covering up . 
