The visual effects for the shifting heads of the Seraphim were created by means of CGI and took visual-effects supervisor Laurie Kallsen-George a long time to complete, who didn't finish until "hours before airtime."
It's the second time, after Die Hand Die Verletzt (1995), that Scully and Mulder have to confront what seems to be genuine Hell's spawn. A third time occurs in Terms of Endearment (1999) when Mulder and Scully come across a demoness who wants to have a demon child. A fourth time occurs in Familiar (2018) when they come across another demon conjured by a housewife in a small town.
Scully's confessional was a last minute addition to the script to flesh out her motivations. The scene was eight pages long.
Emily -- the product of experimentation in the realm of the creation of alien-human hybrids, seems to represent a parallel to the Nephilim, who are described as the offspring of an angel and a mortal woman
When Scully takes Emily's picture from her desk and tearfully looks at it, the piano theme playing is taken directly from Pyotr Ilyich Tchaikovsky's fourth Symphony, 2nd movement.