At the end of the opening credits, "VGhlIFRydXRoIGlzIE91dCBUaGVyZQ=" is a base64 string that decodes to "The Truth is Out There".
The artificial intelligence bot that was tricked into posting racist and insensitive tweets on Twitter on March 23, 2016, as described in the opening prologue, is Microsoft's Tay.
The title "Rm9sbG93ZXJz" is a base64 string that decodes to "Followers." The sushi restaurant where Mulder and Scully eat is named FOROWA, which is the word for Follower in Japanese. The word FOROWA also appears in Japanese characters on the neon sign of the restaurant.
The code on Scully's home security system is 0223, which is her birthday, February 23. Her password 'Queequeg' was also the name of the Pomeranian dog she had in season 3 from Clyde Bruckman's Final Repose (1995) to Quagmire (1996). The name Queequeg is from the classic novel "Moby Dick", which was also where Scully's and her father's nicknames 'Starbuck' and 'Ahab' originate.
Scully's haircut is back to her classic bob starting with this episode. Mulder fails to notice the change for two whole episodes (he asks her if she had gotten a haircut during Nothing Lasts Forever (2018)).