Although Carter initially conceived of the series based on the influence of Kolchak and The Twilight Zone, he has stated that the "leaping-off point" for the series' overall concept came from UFO lore. After being introduced to the works of John E. Mack—especially a study by Mack which had reported that three percent of Americans claimed to have been abducted by aliens—Carter believed he had found his central theme. It was decided that the series would focus on the FBI in order to avoid something Carter had seen as a failing in Kolchak, whereby mysterious events would continually occur in one locale and be accidentally uncovered by the same character—by creating a fictional FBI unit which actively uncovered these paranormal cases, it was felt that the series would be "sustainable week after week without stretching the parameters of credibility". Early in the planning stages, Carter had envisioned that a significant proportion of the episodes would deal with investigations which uncovered hoaxes or cases which had been mistakenly viewed as paranormal. Although this decision never came to pass, the third-season episode "Jose Chung's From Outer Space" can be seen as a holdover from the idea. 
The series revolves around its two main characters, which had been defined early in conception as the "believer" and the "skeptic". Of these, the "believer", Fox Mulder, was created with a character-defining personal motivation, involving the disappearance of his younger sister during his childhood, which he would believe to be a result of alien abduction. The creation of the "skeptic", Dana Scully, was influenced by Jodie Foster's portrayal of Clarice Starling in The Silence of the Lambs, leading the crew to decide that the character needed to seem "real", as opposed to the "bombshell" type of character the studio was pressing for. 
Thematically, although the series focused heavily on alien abduction lore,] the decision was made early on to allow the plots of individual episodes to branch out into different territories in order to prevent the overarching plot from running out of momentum, which led to standalone episodes such as "Squeeze" being developed.] The variety of storylines which the series has shown has led director Daniel Sackheim to note that "The X-Files has sort of found its own style in that it doesn't have a confined style to it", adding that the series' "fluid" approach has meant that "everybody who comes on the show attempt to make a little scary movie". To this end, several episodes feature varying plots, with alien-influenced storylines varying between "Ice", a "briskly-paced" episode set in a single location, and the character-driven "Conduit", which served to fill in background on the characters. Elsewhere, plots focused on soul transference or reincarnation, with the episodes "Shadows", "Born Again" and "Lazarus" sharing similar storylines. The plot of "Ghost in the Machine" featured a malevolent artificial intelligence; while "Shapes" introduced the first of what would become several Native American-themed episodes. 
The first season also introduced a number of minor characters who would go on to become central figures to the series—The Lone Gunmen, first seen in "E.B.E.", would become regular characters beginning the second season, eventually starring in the spin-off series The Lone Gunmen; whilst the episode "Tooms" introduced Walter Skinner, portrayed by Mitch Pileggi, who would go on to be billed as a series star by the ninth season.[12] The abduction of Mulder's sister Samantha was explored in the episodes "Pilot", "Conduit", and "Miracle Man", and would go on to become one of the central themes of the series as a whole.