Several of the elements introduced in the collected episodes arose through necessity during production, as working around the pregnancy of lead actress Gillian Anderson led to both the creation of unifying plot thread and the introduction of several recurring characters.

The episodes in the collection follow the investigations of paranormal-related cases, or X-Files, by FBI Special Agents Fox Mulder (David Duchovny) and Dana Scully (Anderson).

Jerry Hardin, William B. Davis, Mitch Pileggi, Tom Braidwood, Dean Haglund and Bruce Harwood all play supporting roles in the collection.

[5][6] Deep Throat is soon killed, however, when he helps the agents uncover details of a government human cloning program, and the X-Files unit is closed shortly thereafter.

[7][8] Unable to continue his work with Scully, Mulder obtains information about possible extraterrestrial contact in Puerto Rico, finding that the SETI program at the Arecibo Observatory is being forcibly closed.

[16][17][18] The Lone Gunmen contact Mulder and Scully about a successful attempt by a friend of theirs to hack the United States Department of Defense computer system.

Contacting Albert Hosteen (Floyd Red Crow Westerman)—a Navajo man capable of translating the files—Mulder is shown a box-car full of what appear to be alien corpses.

[25] In addition to the creation of the storyline concerning Scully's abduction, Anderson's reduced role in the first half of the second season permitted the writers to develop some of the other characters in the show including Assistant Director Walter Skinner (Mitch Pileggi), The Smoking Man (William B. Davis) and X (Steven Williams), and resulted in the introduction of the character Alex Krycek (Nicholas Lea).

[26] Krycek, who was initially created by writer Howard Gordon to temporarily replace Scully as Mulder's partner for three episodes eventually grew into a character that lasted seven seasons on the show.

It was later revealed to the producers that Davis was running an acting school, and teaching such actors as ninth season guest star Lucy Lawless.

[23] In the two-part story of "Colony" and "End Game", Carter and Spotnitz, along with Duchovny, created what would become a recurring character in the alien bounty hunter.

[30] Writing for IGN, Dan Iverson rated the collection eight out of ten, finding that the mythology-based episodes formed the basis of the relationship between the characters of Mulder and Scully.