The continuing search for Jeremiah Smith leads Scully to uncover encrypted data files whose purpose is not yet known. Being closely hunted by an unknown assassin, Jeremiah leads Mulder to a secluded farm in rural Canada while men in suits determine Mrs. Mulder's fate.

FBI Assistant Director Walter Skinner is the prime suspect in a homicide involving a woman he was with the night of her death. Mulder and Scully are all he has to prove his innocence, as superior officers try to shut him down and the only clue is a mysterious old woman.

After Mulder’s disappearance, Scully returns to FBI headquarters to find Special Agent John Doggett heading up a FBI manhunt for her partner. Knowing that type of search will prove futile, Scully and Skinner turn to the Lone Gunmen in hopes of uncovering information about additional UFO activity around the time of Mulder’s disappearance. Although such information leads them to Gibson Praise, the man with Gibson, a man who appears to be Mulder, is in fact an alien bounty hunter. Finally realizing that Mulder will not be found so easily, Agent Doggett is officially assigned to the X-Files. Now, after all she has been through with Mulder, it is Scully who is “the believer” and who must find a way to work with “the skeptic,” John Doggett.

Aware his presence only puts Scully and William in jeopardy Mulder once again disappears — but at least this time it is his own choice. A frustrated Agent Doggett tries to find Mulder so he can proceed with his investigation against Deputy Director Kersh, but Scully and Skinner finally convince him to drop his case. Yet even as Scully helps Agent Doggett and Agent Reyes on some of their cases she realizes William is still in danger. When she learns a religious cult wants her son dead she turns to the Lone Gunmen. But even they cannot prevent William from being kidnapped, a fact which forces Scully to make a painful decision. Yet even in her darkest hour she receives word that Mulder has been found — and is being held in a military brig for the murder of a man who cannot die.

As Mulder lies in a neurological unit, his brain under attack by a deadly onslaught of electrical impulses, Scully struggles to decipher strange symbols covering a spacecraft found submerged off West Africa's Ivory Coast. But the connection between these two phenomena is just the first of many challenges the agents are destined to confront. For they are about to enter a time of closure and a time of new beginnings. For Mulder there's the death of his mother and Diana Fowley, and the end of his search for his abducted sister, Samantha. For Scully it is a time to face her own personal demons, among them the return of death fetishist Donnie Pfaster. Yet just as Scully faces the ultimate new beginning, the ultimate horror occurs — the abduction of Mulder.

When a terrorist bomb destroys a building in Dallas, Texas FBI agents Fox Mulder and Dana Scully are drawn into a dangerous conspiracy surpassing anything they’ve ever encountered. With the dubious assistance of a paranoid doctor, Mulder and Scully risk their careers and their lives to hunt down a deadly virus which may be extraterrestrial in origin — and could destroy all life on Earth.

Even as Scully’s genetically altered DNA brings her closer to the brink of death, government agent Michael Kritschgau helps Mulder in the search for a cure, partly to atone for his own involvement with perpetrating the alien hoax. Scully’s DNA comes into play once again when she discovers she is the mother of a little girl named Emily, an incident that could only be related to her abduction years earlier. But in the end it is a young boy named Gibson Praise whose body may contain genetic proof of man’s relationship to an alien race — and who may hold the key to unlocking the mysteries of the X-Files.

The X-Files has been shut down and Mulder and Scully are separated. Scully finds herself teaching classes at the FBI Academy in Quantico, Virginia, while Mulder is assigned to surveillance duty. With Agent Alex Krycek as his new partner, and the mysterious X as his new source of information, Mulder struggles to keep his search for the truth alive. But ironically it is Scully who experiences the close encounter Mulder has longed for, taking a journey that will ultimately bring the two agents back together and forging a bond that will make them closer than ever before.

Mulder and Scully are called back to duty by the FBI when a former priest claims to be receiving psychic visions pertaining to a kidnapped agent.

The first season introduced main characters of the series, including Fox Mulder and Dana Scully who were portrayed by David Duchovny and Gillian Anderson respectively, and recurring characters Deep Throat, Walter Skinner and The Smoking Man. The season introduced the series' main concept, revolving around the investigation of paranormal or supernatural cases, known as X-Files, by the Federal Bureau of Investigation; it also began to lay the groundwork for the series' overarching mythology. Initially influenced by Kolchak: The Night Stalker and The Twilight Zone, series creator Chris Carter pitched the idea for the series to Fox twice before it was accepted for production. The season saw the series quickly gaining popularity, with ratings rising steadily throughout its run; and garnered generally positive reviews from critics and the media. It helped to make stars of its two lead roles, and several of its taglines and catchphrases have since become cultural staples.

1998 film by Rob Bowman