Written by executive producer Chris Carter and directed by R. W. Goodwin, the episode continues with the mythology story arc which started with "Pilot".
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.
"The Erlenmeyer Flask" introduced several new plot elements which would continue in later seasons and featured the death of recurring character "Deep Throat" (Jerry Hardin).
Soon afterwards, Deep Throat (Jerry Hardin) approaches Fox Mulder with Secare's case, saying he is of major importance to revealing the truth.
When investigating the case, Mulder and Dana Scully visit Dr. Terrance Berube (Ken Kramer), a scientist working in Gaithersburg whose car was being driven by Secare.
Carpenter reveals that the "Purity Control" flask contains a sample of bacteria that doesn't exist anywhere in nature and can only be described as extraterrestrial.
At an exchange on a freeway overpass, Deep Throat presents the fetus to the Crew Cut Man, who shoots him seconds later.
Meanwhile, in a scene mirroring the conclusion to the pilot, the Smoking Man stores the alien fetus in the massive evidence room within the Pentagon.
He tried to firmly establish the mythology of the series, "where we explored the different avenues of government conspiracy, and turning it into more than just flying saucers", and having what the writer called a "defining moment" for Scully, where the agent would hear from a fellow scientist that she was dealing with truly extraterrestrial material.
[3] The scene where poisonous fumes were emitted by Dr. Secare was inspired by the case of Gloria Ramirez, which occurred in California in February 1994; Carter remembered this when writing the script, and it became an established aspect of the mythology in subsequent seasons.
The decision to shut down the X-Files was done to separate the agents, allowing the producers to work around Gillian Anderson's pregnancy (which contributed to an important plot development in the second season and affected the rest of the series).
[5] The Fox network initially opposed the idea, fearing that closing down the X-Files would lead viewers to believe that the show had been cancelled.
[6] The ending of this episode mirrors that of the "Pilot", including Mulder calling Scully at 11:21 pm and the Smoking Man storing evidence in the Pentagon.
[8] Executive producer R. W. Goodwin decided to make his directorial debut with the episode, as he considered it "the best script by far", offering "a combination of elation and stark terror".
[12] John Keegan from Critical Myth gave the episode 9 out of 10, saying it was "the perfect ending to the first season" and a good introduction to The X-Files mythology.