Scully can be seen handling the two coins fused together from Dreamland (1998) and the dog tag from Quagmire (1996). She also gives Doggett the Apollo 11 medallion from Max (1997). Agent Leyla Harrison mentions that their suspect may be "a liver eating mutant", saying that Mulder and Scully have killed one. This is a reference to Squeeze (1993) and Tooms (1994).
The character Leyla Harrison, who appeared in episodes Alone (2001) and Scary Monsters (2002) was named after a writer of The X-Files (1993) internet fanfiction who died of cancer in February 2001. The fictional Leyla Harrison was a fan of Mulder's and Scully's, having spent her time in the FBI poring over their expense reports (in much the same way that internet fans of the show examined the minute nuances of every episode), so the tribute was very appropriate.
The production team had yet to hear from 20th Century Fox as to whether they would greenlight a ninth season of the show so Frank Spotnitz wrote this with the expectation that it would be the last monster of the week episode in the series. To that end, Agent Leyla Harrison was created as a thank you from the fandom to the characters of Mulder and Scully.
The final scene in which Mulder and Scully bicker about how they got back from Antarctica took longer to film because the other actor in the scene (Jolie Jenkins) couldn't stop laughing at her co-stars.
This was the first time that Jolie Jenkins had ever handled a gun before, perfect for her character who was pretty much in the same boat.