Scully is asked to report on the case and to give her impressions of Mulder. She tells them that she believes Agent Mulder's assertions but can't substantiate them. "Agent Mulder believes we are not alone." Deep Throat contacts Mulder again and tells him that he can try to help them but their lives are in danger. Mulder says, "They're here aren't they?", to which Deep Throat replies, "Mr. Mulder, THEY have been here a very, very long time." "I want to believe...". Deep Throat meets with the chairman and tells him that it is more dangerous to let Mulder loose, free to tell what he knows. When confronted he reveals to Mulder a secret pact between several nations whereby any surviving EBE would be exterminated and that he was among only three men to have carried those orders out. although they release Mulder, they kill Deep Throat and drive away. Scully rushes to his aid in vain, and his last words are "Trust No One". Two weeks later, Mulder calls Scully to tell her that the X-Files division has been shutdown

Pilot Episode Scully is assigned to the X-Files division by the FBI section chief while the Cigarette Smoking Man stands by wordlessly watching. Mulder believes her to be sent to spy on him but quickly comes to trust her. He tells her the story of his sister's abduction and his newfound interest in the X-Files and the Truth they might hold. He has made this search for the Truth his quest and motivation in life. The case is one of suspected alien abduction and the body of one victim reveals a metallic implant in the nasal cavity. The body itself no longer resembles the human it is supposed to be and Scully and Mulder collect lots of forensic evidence to support their claims. Unfortunately, by the end of the episode, all of their evidence has been destroyed in a fire and they are no closer to Mulder's Truth than they were at the beginning. Scully did manage to keep the metallic implant but on the conclusion of their case she hands it over to her superiors as proof and it is conveniently filed in an underground warehouse in the Pentagon which apparently holds many such instances of evidence. Scully is asked to report on the case and to give her impressions of Mulder. She tells them that she believes Agent Mulder's assertions but can't substantiate them. "Agent Mulder believes we are not alone." Deep Throat In this second episode, Mulder is contacted by a mysterious government insider who offers him vague clues and information but warns him against pursuing his current case regarding secret UFO technology at a government installation. Mulder doesn't share this warning with Scully and instead proceeds on the case. It appears that the sightings are substantial but after being warned off the case by some MIBs (Men in Black), Scully is convinced that they shouldn't pursue the case. Mulder goes alone to the government airfield and actually sees a triangular craft unlike any technology the Air Force Base has. But no sooner has he witnessed this proof than he is captured and drugged. When he is returned to Scully, he is unaware of his surroundings and has no recollection of what he's seen. Deep Throat contacts Mulder again and tells him that he can try to help them but their lives are in danger. Mulder says, "They're here aren't they?", to which Deep Throat replies, "Mr. Mulder, THEY have been here a very, very long time." Conduit Mulder gets ahold of a case concerning an apparent abduction of a teenage girl. The case reminds him of his sister and her mysterious disappearance and he recounts the event to Scully. The end of the episode finds Mulder in a church remembering his sister and the painful memories the case has brought to the surface while Scully listens to the tapes of Mulder's hypnotic regression sessions. As she was being taken from him he remembers her calling his name while another voice told him that his sister would be okay. When asked if he believed the voice he replied, "I want to believe...". Fallen Angel Mulder is contacted by Deep Throat regarding a government evacuation of a toxic spill which he tells him is really a UFO retrieval team who will have "sanitized" the area in 24 hours. Mulder heads directly to the site without informing or bringing along Scully. He is found at the site by the retrieval team while trying to snap pictures and is thrown into a detention cell where Scully finds him the next day. She is still trying to convince herself of the veracity of the governments cover story while Mulder knows the evidence his own eyes saw...a downed UFO or "fallen angel". Scully has come to bring Mulder back to Washington where they are scheduled to go before a review board who are not happy with the agent's behavior and are threatening to shutdown the X-Files. The committee, after grilling Mulder and Scully, are certain to shut down the X-Files until Deep Throat meets with the chairman and tells him that it is more dangerous to let Mulder loose, free to tell what he knows. E.B.E. A pilot shoots down a UFO which crashes near a US installation in Iraq. When a truck driver in Tennessee says he saw lights and a UFO and lost power, Mulder is convinced that the truck was transporting an EBE (extraterrestrial biological entity) across the country. Deep Throat contacts Mulder with information but Scully is skeptical of his honesty and true willingness to help them. She feels that Mulder is too eager to accept his information at face value. It turns out that Deep Throat had given the agents false information to divert them from the true operation. When confronted he reveals to Mulder a secret pact between several nations whereby any surviving EBE would be exterminated and that he was among only three men to have carried those orders out. This is the reason behind his desire to help Mulder, as a form of atonement. Erlenmeyer Flask (season one finale) A case is brought to the attention of Mulder by Deep Throat. On the surface it appears to be a fugitive from a high speed car chase who is still evading capture although he had been shot before diving into the water. It becomes clear that the fugitive is the product of experimentation with alien DNA in humans that affords them healing and curative powers, and the ability to breathe under water, which is how the man evaded capture and discovery. Mulder and Scully track down a scientist who seems to be involved in the experiments only to find him dead. A sample of his work reveals DNA sequence found nowhere in nature...by definition, extraterrestrial. In the course of the episode, all the scientists with information, all the people being experimented on, and all the evidence is eliminated. Mulder is caught and kidnapped by the clean-up team and Deep Throat contacts Scully with a plan to barter for his safe release. He says he can provide Scully with ID to gain access to the original alien tissue used in the experiments and he will trade that for Mulder's life. Scully retrieves an alien fetus and Deep Throat sets up a meet but, although they release Mulder, they kill Deep Throat and drive away. Scully rushes to his aid in vain, and his last words are "Trust No One". Two weeks later, Mulder calls Scully to tell her that the X-Files division has been shutdown and that they have both been reassigned. But Mulder says he won't give up...not if the truth is out there. Coming full circle from the pilot episode, the season finale ends with the Cigarette Smoking Man entering the basement warehouse in the Pentagon and depositing the alien fetus in a box with several similar containers.