The show centers on FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) who work on cases linked to the paranormal, called X-Files.

In this episode, Mulder returns from Hong Kong, having found rogue agent Alex Krycek (Nicholas Lea) while investigating a mysterious mind-altering black oil.

On August 19, 1953, a burned crewman talks to three government agents about his experience on the submarine Zeus Faber, completing the story told in the previous episode.

In the present, Fox Mulder and Alex Krycek return to the United States, but are run off the road by another vehicle.

Dana Scully tells Mulder about Walter Skinner's condition, and says that an analysis of saliva has identified his shooter as the same person who killed her sister Melissa.

Krycek, possessed by the black oil, returns the tape to the Smoking Man in exchange for the location of the recovered UFO.

As Luis Cardinal is identified as Skinner's shooter, the Syndicate admonishes the Smoking Man for moving the UFO to a new location.

By rubbing a pencil over the envelope containing the tape case, Mulder finds a phone number which connects him to the Syndicate's office.

[1][2] Conception of the episode was based around a visual image series creator Chris Carter had wanted to include in a script "since the beginning of the show".

[6] Nicholas Lea was fitted with a mask with tubes for the scene where the alien black oil leaves his body.

To fix this, the sound stage used to represent the submarine's interior was rebuilt so it could be rocked back and forth, with the movement being used to guide the flow of a different liquid.

[8] The black oil effect over people's eyes was accomplished by inserting the footage digitally in post production.

The review noted that the episode offered "some interesting progressions in the grand theme" of the series, although it was also "worth it just for the awesome missile site finale" alone.

[13] Terrorist Timothy McVeigh, a fan of The X-Files, asked his defense team to watch the episode "Apocrypha" with him to showcase its "covert meetings in the night, secret goings-on" and "ghost government."