The character Leyla Harrison, who appeared in Alone (2001) and Scary Monsters, was named after a writer of X-Files Internet fan fiction 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.
Among other items of Agent Mulder at Scully's apartment is Mulder's fish tank.
Tommy Conlon shows Special Agent Monica Reyes a picture he drew and says, "I made this". This is just like the voiceover of the X-Files credit for production company Ten Thirteen.
Chris Carter traveled to the episode's location to personally break the news to the cast and crew that the show had been canceled by Fox. (The broadcast order of Season 9's episodes is very different to the production order.)