Mulder's first encounter with Deep Throat was to receive a warning from him to stay away from Ellens Air Force Base, this, of course, immediately intrigues Mulder and he does the exact opposite. Deep Throat shares information with Scully and Mulder to entice them into cases that they might otherwise overlook or to draw them away from things they should not know of. When Scully & Mulder begin tracking a truck which may or may not be carrying an E.B.E. across America, Deep Throat attempts to lead them away the case. The ploy does not work, and Mulder finds out the truth about Deep Throat. He is a part of an organisation which has a directive that calls for the systematic and immediate termination of any alien life form that is encountered. Deep Throat reveals that he has carried out this directive at least once.

Deep Throat's primary motivation in his contact with Mulder seems to be his own guilt over what he has done. He states that the organization that he belongs to has committed "heinous acts against man". It's probable he is referring to the experiments carried out on human abductees. When Mulder & Scully are about a drop a case concerning a fugitive with green blood because of a lack of information, Deep Throat intervenes to tell him to continue to investigate the case because it may be more important than it first seems. Mulder risks his life to protect to fugitive and Deep Throat has to make an important exchange to save Mulder even though he knows he will in all likelihood be killed. Deep Throat is executed but Mulder is released. These events result in the closure of the x-files by Assistant Director Skinner.