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, a French salvage ship sends a diving crew to recover a mysterious wreckage from World War II, but the crew falls prey to a bizarre illness forcing FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) to investigate the source.

"Piper Maru" was written to showcase two visual images Chris Carter had wanted to include in a script "since the beginning of the show".

The first of these was that of a deep-sea diver finding a still-living pilot trapped in the wreckage of a World War II-era fighter plane and the second was that of a black-and-white flashback taking place in a submarine.

Gauthier, a member of the ship's crew, dives down into the sea and finds a sunken fighter plane from World War II.

In Washington, Walter Skinner tells Dana Scully that the FBI's investigation into her sister's murder has been made inactive, despite the evidence that had been recovered.

Arriving at her office, he finds Alex Krycek (Nicholas Lea) waiting inside, having been selling the contents of the digital tape.

Meanwhile, Skinner is initially confronted in a restaurant by several men, including the Gray-Haired Man, and is told not to pursue Melissa Scully's case any further.

[1][2] Conception of the episode originated in two visual images series creator Chris Carter had wanted to include in a script "since the beginning of the show".

[3] The first of these was that of a deep-sea diver finding a still-living pilot trapped in the wreckage of a World War II-era fighter plane; and the second was that of a black-and-white flashback taking place in a submarine.

[4] Director Rob Bowman shared with Carter his experiences diving, feeling that an episode based on finding "something creepy" underwater would be a good idea.

Spotnitz ended up writing his ideas on a magazine, not having brought paper with him, and included in his outline the investigation of Scully's sister's murder and the reintroduction of Alex Krycek.

[8] Bowman also reshot the episode's ending, as originally Duchovny and Lea were to walk past the camera and continue off-screen.

Feeling this was not effective, he replaced this with a walking shot which continued straight towards and into the camera, noting that "Nick will jump in front of a truck if he think it will make a scene better".

The review described "Piper Maru" as featuring "a tough and sentimental Scully", noting that "action-packed detective work by Mulder enhance[s] an already crackling scenario.

"[17] Nick De Semlyen and James White of Empire named it the sixth "greatest" episode of the series, describing it as "thrilling", "pacey" and "balanced".