 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.