 The Smoking Man meets with the Syndicate , who are responsible for the bees . Soon afterward a swarm of bees attacks a school in Columbia , South Carolina , and one of the teachers dies as a result . Skinner heads to the hospital , where he is met by Covarrubias . She demands to know what he knows about the matter . He tells her he believes that the bees are being used as a carrier for some sort of experiment . Skinner returns home where he is confronted by Mulder , who now suspects that Skinner has been working against him all this time . Skinner is able to convince Mulder that he would not have forced his own drawer lock open and hence could not have been the murderer . Convinced of Skinner 's evidence , Mulder turns in the gun with the serial number filed off so Skinner is not blamed for the murder . That night Skinner confronts The Smoking Man in his apartment , angry that nothing has been done for Scully . The Smoking Man convinces him that Scully will die if he kills him and Skinner leaves without killing him , but not before firing warning shots . Shortly afterwards Covarrubias calls The Smoking Man , who tells her to tell Mulder what he wants to hear while an unknown man is shown behind her listening on another phone . 
