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 and Scully investigate information gleaned from secret government records, finding that a Nazi scientist working as part of Operation Paperclip may have been responsible for creating a race of human-alien hybrids.

Continuing from the previous episode, Dana Scully (Gillian Anderson) and Walter Skinner (Mitch Pileggi) hold each other at gunpoint.

The agents visit The Lone Gunmen, showing them an old photo featuring Bill Mulder, The Smoking Man, Deep Throat and other members of the Syndicate.

The Lone Gunmen also recognize Victor Klemper, a notorious Nazi scientist who was brought to the United States under Operation Paperclip.

Mulder and Scully arrive at the mining facility and, using the code for Napier's constant given to them by Klemper, unlock one of the reinforced doors inside.

Hearing noise, Mulder heads outside and witnesses a UFO flying overhead; inside, small beings run past Scully.

Skinner chases the man into a stairwell, where he is attacked by Alex Krycek and Luis Cardinal, who beat him unconscious and steal the tape.

The Smoking Man lies to the rest of the Syndicate, telling them that Scully's would-be assassin was killed in the car bombing and that the tape has been destroyed with him.

[3] As the episode proceeds, his scientific pursuits soon begin to paint him as the archetypal scientist who "goes too far", a serious factor Delasara argues "'alienates' [the public] further from science and its practitioners".

The mining facility is named for Dr. Hubertus Strughold, a real-life German scientist who was employed by the United States after World War II.

The name is almost identical to a Victor Klemperer who was a German Jew that escaped persecution during World War II by fleeing to American-controlled territory.

[6] In 1996 Mitch Pileggi called the episode one of the show's finest, particularly enjoying the line where he tells The Smoking Man to "pucker up and kiss my ass".

[8] "Paper Clip" is one of the defining episodes of The X-Files because it simultaneously expands the conspiracy into the kind of giant you can never hope to fight and brings it down to a more prosaic level.

The Cigarette Smoking Man is a multi-tentacled monster with his hands in everything that's out there, but he can also be defeated by a resourceful FBI director and a bunch of guys with top-notch memorization skills.

It was called an "outstanding episode", although Scully's unwillingness to accept the paranormal after making contact was seen as "exacerbat[ing] a maddening trend".

She felt that its strengths came from its parallels with real world history, such as its handling of Operation Paperclip and the actions of the West during the Cold War, noting that "the compromises the United States and other Western nations made to survive the onslaught of communism in the Cold War were ones that should have made more of those nations' citizens take pause, stop to think about the cost of living free, but they almost never did".