In the FBI Headquarters, Mulder talks to Scully about the Philadelphia Experiment. According to this urban legend, this was a series of secret experiments made in 1943 by the U.S. Navy to manipulate electromagnetic fields, making a ship (USS Eldridge) invisible to enemy radar. This story line was used in The Philadelphia Experiment (1984).
When Scully is writing in the notebook aboard the ship, she mentions Ragnarok. It's the name of the apocalypse created by the old Norse/vikings centuries ago. In it, the sun should be eaten by a giant wolf called Fenrir, and the demons imprisoned by Odin at the dawn of times in a hellish called Muspell should be free, and lead by a demon named Surtur should launch the definitive attack to kill all gods and dead warriors who have inhabited Valhalla, causing the end of days.
The sailor in the locker whom Mulder and Scully find is holding what looks like a Jack Daniel's Old no.7 Tennessee Whiskey bottle. The label actually says Jim Dandie's Old no. 2 Kentucky Whiskey (also used in Wolfcop (2014)).
When Mulder shows Scully the map that charts all the voyages that passed through the 65th parallel, she says to him, "Another Bermuda Triangle?" to which he replies,"More like 'A Wrinkle In Time'." He is referencing the 1962 Science Fiction book of the same name by Madeleine L'Engle.
The Norwegian town Mulder and Scully go to, Tildeskan, is fictional.