The actual Operation Crossroads was a series of atomic bomb tests at the Bikini Atoll in 1946. A variety of surplus World War II ships were used as targets to demonstrate the effects of nearby atomic explosions.
Jackson van de Kamp's blog username is @rever: French for "to dream", Portuguese for "to see again".
A case of "creepypasta" coming to life would be that of the "Slender Man" in the United States, which may or may not be the inspiration for this installment of the X-files. In the case of "Slender Man", two Wisconsin girls try to murder their fellow classmate in order to impress the fictional character so that they might reside in his home in the woods.
The blue and white ferry boat called the "Chimera" is actually the "Queen of Sidney" and is awaiting salvage near the town of Mission, British Columbia, Canada. The same ship has been used in other shows, such as Supernatural, specifically episodes The Bad Place (2017) and Wayward Sisters (2018).
It turns out that, when he's in coffee shops, Mulder uses the name Bob because he's fed up trying to explain the name, Fox.