The show centers on FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) who work on cases linked to the paranormal, called X-Files.

What they find seems to support Mulder's revived belief in aliens, but is discredited when the agents are not reassigned to the now re-opened X-Files, with Jeffrey Spender (Chris Owens) and Diana Fowley (Mimi Rogers) taking over instead.

"The Beginning" was the first episode of the series to not be filmed in Vancouver, Canada, after production was moved to Los Angeles at the behest of lead actor David Duchovny.

The writers sought to bring back characters, such as Spender, Fowley, and Gibson Praise (Jeff Gulka) who had not been featured in the movie, but had played a pivotal role in the show's fifth season.

In Phoenix, Arizona, a scientist working for Roush Technologies is exposed to the black oil; an alien creature gestates and bursts from his body the next morning.

The move was instigated by David Duchovny, who portrayed Mulder, in order to increase his opportunity to find movie work as well as to give him a chance to be nearer to his wife, Téa Leoni.

[2][3] According to Andy Meisler, "The very first shot of the season a long look directly into a bright sun shining on a barren desert was designed to boldly announce the show's arrival in Southern California.

"[4] As a result of the move, the episode featured a largely new group of crew members, hired by Carter, Frank Spotnitz and new co-executive producer Michael Watkins; this necessitated the show's new crewmembers spending five weeks, receiving, unpacking, and cataloging filming material from their Vancouver counterparts.

Many accused the show of "Hollywood-izing" the series by adding notable guest stars as well as making the plots simpler and more enjoyable for larger audiences.

[5] Spotnitz said that the hardest part about writing "The Beginning" was the task of not only segueing from a movie but also tying the story into the previous season finale.

[4] The character Sandy, who is killed in the teaser sequence, was played by the show's casting director Rick Millikan at the request of Carter.

"[6] The scenes set in the nuclear power plant were filmed in a Long Beach, California-based building owned by the electricity supply company Southern California Edison.

[6] The scenes of the alien molting in the power plant's spent fuel pool were filmed in a tank of water located in Marina del Rey, California that was frequently used by the producers of the show Baywatch.

5, author Andy Meisler wrote that some fans and critics responded positively to "The Beginning," most notably because the episode functioned as "a particularly artful and effective way to launch the series's new season—and era.

[14] VanDerWerff's main issue with the entry was that it chose to wrap up the plot thread left dangling with the fifth-season finale, but did little to expand upon the revelations of the series' feature film.

Robert Shearman and Lars Pearson, in their book Wanting to Believe: A Critical Guide to The X-Files, Millennium & The Lone Gunmen, rated the episode one star out of five, writing that "'The Beginning' opens witty enough […] and then offers the viewer no substance.