The episode's teleplay was written by Frank Spotnitz and John Shiban, from a story by Dan Angel and Billy Brown; it was directed by Allen Coulter.

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.

In this episode, the unexplained death of mentally and physically disabled girl prompts Father McCue (Arnie Walters) to ask Scully for her help, but her investigation leads her to a mystery involving Nephilim—children of mortal women and angels.

Scully soon learns that Aaron Starkey (Glenn Morshower), a department of social services worker and demon in disguise, is after the girls, in order that the Devil may control their power.

Shiban and Spotnitz, however, overhauled the idea and added elements extrapolated from the season's earlier "Christmas Carol" and "Emily" two-parter, making "All Souls" the "unofficial third part" of its story arc.

After they viewed the final cut of the installment, Shiban and Spotnitz decided to frame the action around Scully confessing her story to a priest in a confessional.

In Alexandria, Virginia, sixteen-year-old Dara Kernof (Emily Perkins), a mentally and physically disabled girl who uses a wheelchair, somehow manages to leave her house in the middle of the night, soon after her baptism.

Eventually, Dana Scully (Gillian Anderson) is contacted by Father McCue (Arnie Walters), who asks if she would be willing to assist the family in figuring out what exactly happened.

Under questioning by Mulder and Scully, Father Gregory insists that he was attempting to ward off the Devil, who was hoping to claim the girls' souls.

[2] The original genesis for the episode was an idea developed by Dan Angel and Billy Brown, two story board editors for the series that had left after Christmas of 1997.

"[3] Shiban and Spotnitz decided to overhaul the script and feature elements of the earlier "Christmas Carol" and "Emily" story arc, as the writers wanted to include the "very universal" idea of Scully exploring feelings for her deceased daughter.

[3] In order to counter some of the darker aspects of the script, Shiban and Spotnitz—on the behest of co-star David Duchovny—added several lines of comic relief, delivered by Mulder.

The book that Father McCue has about Nephilim was created by assistant art director Vivien Nishi with guidance from Spotnitz.

Makeup artist Laverne Basham and hairstylist Anji Bemben were tasked with giving each of the quadruplets, all played by Emily Perkins, a different look.

On the day of filming, however, she was sent a number of rewrites and subsequently demanded more time to become familiar with the new script, so as to not rush or undermine the emotion she was supposed to put into the scene.

Despite calling the entry "an occasionally too-slow episode", VanDerWerff praised Anderson, lauding her performance as "another […] potential Emmy tape in a season full of them".

[9] Furthermore, she enjoyed the juxtaposition of Scully's skepticism and her religious beliefs, noting that the series could have taken the idea into the realm of irony, but instead played it "with a deathly seriousness" that allowed it to work.

"[10] 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.