"The Erlenmeyer Flask"
Written by Chris Carter
Directed by R. W. Goodwin

In which Mulder and Scully are drawn into the investigation of a missing scientist by their informant, leading to the revelation of hidden experiments and the possible end to the X-Files...

Synopsis - Analysis - Memorable Quotes - Observations




As the episode begins, police officers chase down a man in a car near the shipworks of Arlis, Maryland. The man crashes his car and runs for it, but the police catch up to him. After a vicious scuffle, the man breaks free and runs for the docks. The officers shoot at him, but the man just runs off the end of the dock into the water. When the officers check the dock, sure they wounded the man, they only find some strange puddles of green liquid.

Later that night, Mulder is awakened by the sound of his phone ringing. When he answers, his informant (from “Deep Throat”) tells him to watch a local news channel about the search for the wounded man. Mulder videotapes it and brings it to the office the next morning for Scully to see. Scully thinks the informant is just playing games, but Mulder is certain that there’s something odd that he’s missing.

The agents go to speak with the officer in charge of the search. Some of the video captures Mulder made are of federal agents that have already been working the case, though the officer doesn’t know why. Mulder wants to know why the body hasn’t been recovered after 18 hours in the water, but there are no answers to give. Finally, Mulder asks where the suspect’s car was impounded.

When they find the car, it doesn’t match the vehicle shown in the newscasts. Scully recognizes a caduceus sticker in the windshield of the car in the video captures. They manage to get a partial license plate number from Mulder’s videotape and ask Danny to run a check.

The results send the agents to the Emgen Corporation in Gaithersburg, Maryland, where they find a man named Doctor Berube. Berube is working with animal test subjects and a strange red liquid in an Erlenmeyer flask. The animals appear to be a bit jumpy. Berube claims ignorance concerning the apparent illegal use of his car, and evades any questions about his work.

When Mulder wants to pursue possible leads on the driver of the car, Scully balks. She’s positive that they are wasting their time chasing down leads that will end up going nowhere, and she thinks that Mulder is letting his desire to uncover the truth distort his judgment. Mulder, however, defends his informant, saying that the man needs to be careful in his position.

Still, Mulder goes home, only to be confronted by his informant, who is less than pleased with his diminished sense of commitment. The informant claims that Mulder is on the brink of an important discovery, but Mulder confronts him with Scully’s suspicions. Before Mulder can walk away, his informant tells him, quite simply, that he’s never been closer.

Meanwhile, at Emgen, Berube is confronted by an unidentified man with a crewcut. The man with the crewcut is sure that the missing man, Doctor Secare, contacted Berube, but the scientist denies it. Berube also tells the man with the crewcut that he’s already answered the FBI’s questions. With no answers forthcoming, the man with the crewcut kills Berube. At the same time, as the police call off the search, Secare emerges from the water nearby.

The next morning, Mulder and Scully arrive on the scene of Berube’s death, which has been ruled a suicide. But both of the agents recognize that Berube’s death was staged to look that way. Scully notes that Berube was working on the Human Genome Project, but that doesn’t give her any clue as to his importance. Mulder, however, checks the Erlenmeyer flask that Berube had been working with, and finds the bottom labeled “Purity Control”. He asks Scully to run an analysis on the contents of the flask while he looks into Berube’s background.

While Mulder breaks into Berube’s house and starts looking around, Scully takes a sample from the flask to Dr. Carpenter of Georgetown University. Carpenter determines that the flask contents are some kind of large, oddly-shaped whitish-green bacteria. They decide to run a freeze-fracture test on the bacteria for identification.

Over at Berube’s house, Mulder finds phone records and has Danny run a check on a number called several dozen times. As he waits for a reply, Secare calls, thinking that he’s talking to Berube. Secare is wounded and looking for help, but Mulder is unable to get the man to give his location before a passerby hangs up to call an ambulance. Soon after, Danny calls back with the address for the phone number: a place called Zeus Storage. All the while, the man with the crewcut listens from the street.

The requested ambulance picks up Secare, but on the way to the hospital, they try to relieve the pressure in his chest. The procedure releases some kind of gas, which choke and blind the EMTs. After the ambulance crashes, Secare escapes and runs into the night.

Scully calls Mulder, who is on his way to Zeus Storage. She tells him what Dr. Carpenter discovered. The large bacteria appear to contain a virus of some kind, as well as chloroplasts from plant tissue. It all suggests some kind of gene therapy, but nothing familiar to Carpenter. Scully underscores just how unusual the contents of the flask are, and how rare they must be.

Mulder hangs up when he arrives at Zeus Storage. Using a set of keys from Berube’s house, he finds the storage room the scientist was maintaining. Inside he finds five men in large aquariums filled with water. Each man is hooked up to a computer for observation, and they are all alive, breathing underwater.

Meanwhile, Dr. Carpenter wakes Scully at the university. A DNA test on the bacteria yielded six DNA base pairs instead of the known four, which leads the scientist to conclude that the bacteria must be, by definition, extraterrestrial. At the same time, as Mulder leaves the storage building, he is chased off by three men.

The next morning, when Mulder finally gets home, Scully contacts him with the information on the bacteria. Mulder accepts that (and her apology for doubting him), and takes her to see the storage room. But when they arrive, everything is gone. Before they can decide what to do, their informant walks in. claiming that the evidence and test subjects must have been destroyed.

The informant explains that the men in the experiment were the culmination of decades of hybridization experiments with alien DNA from a virus. Using recovered tissue from several crashes since 1947, they’ve been working on a hybrid. Berube was the first to succeed in any real sense, and for that very reason, the experiments were to be destroyed. But one of the subjects, Secare, was a friend of Berube’s, and was warned. So Secare escaped before he could be killed.

Mulder goes to look for Secare, while Scully follows up on the analysis of the flask contents. But she finds that Dr. Carpenter has been killed in a “car accident”. Mulder tracks down Secare at Berube’s house, but before he can convince Secare to trust him, the man with the crewcut shoots Secare in the back of the neck. Mulder is exposed as green liquid pours out of the wound, and he is soon unconscious, nasty red sores around his eyes, nose, and mouth.

Mulder awakens sometime later, bound by the man with the crewcut. Secare’s body is being removed. Mulder’s cell phone is ringing off the hook, but Mulder refuses to answer, not wanting to let the man with the crewcut know who’s calling.

Scully, who’s been trying to call, goes to Mulder’s apartment, where she’s met by the informant. The informant is sure that Mulder is alive, and that Scully can use the evidence they have to trade for Mulder’s life. Scully points out that they have no evidence, but the informant explains that he can get Scully access to something valuable: the original tissue source for the alien DNA.

Using the falsified pass provided by the informant, Scully gets access to a high containment facility on Fort Marlene. She manages to get into a room marked “Purity Control”, and she opens a cryogenic chamber. When she takes a look at the contents, it appears to be a fetus of alien origin.

Somehow, she leaves the facility with the fetus, and meets with the informant, who has set up a trade. The informant insists on being the one to hand over the fetus, and Scully agrees reluctantly. On her way back to her car, she takes note of the driver of the van bringing Mulder. It’s the man with the crewcut.

As Scully watches in her rear-view mirror, the informant hands over the fetus, and is promptly shot in the chest. Scully runs from her car to check on him as the van pulls away, dumping Mulder out the back as it speeds off. Mulder is hurt but alive. When Scully checks on the informant, however, the man is clearly dying. His last words to her: “Trust no one.”

Thirteen days later, Mulder calls Scully late at night to inform her that the X-Files have been shut down by Assistant Director Skinner. They are both going to be reassigned to separate sections. Apparently the top levels of the executive branch made the decision. Scully is shocked that Mulder would give up the fight, but he promises her that he’ll still be searching for the truth, no matter what it takes.

Meanwhile, in the vast storage room last seen in “Pilot”, the cigarette-smoking man takes the fetus (now in a jar) and places it into storage. The storage container holds several other jars with identical contents. As he leaves, an emergency placard on the door reveals the room’s location: the Pentagon.


As season finales go, this one took the series to an entirely new level. Picking up the threads from the entire season, as well as the growing threat from Skinner to the X-Files, this episode introduced elements of the series mythology that would take more than four seasons to explain. Even so, there are aspects of this episode that are still difficult to decipher, despite the revelations that have come since its original airing.

As exciting as this episode is, like many of the first season episodes devoted to the emerging mythology, there are some plot oddities that don’t quite add up. Most of those oddities surround the informant and his motivations. The informant continues to claim that his goal is to show Mulder the truth, but at the same time, he intentionally withholds information needed to properly interpret what Mulder’s investigating.

More than that, the informant’s explanation for the experiments doesn’t quite tell the whole story. While it’s likely that the experiments were, in fact, related to the hybridization phase of the project, he doesn’t adequately explain why the experiments needed to be destroyed.

It’s explained in the sixth season episode “Two Fathers” that the experiments were conducted because the Syndicate behind the conspiracy had offered to use gene therapy techniques to “hybridize” themselves, so they could be slave labor for the alien Colonists (the black oil virus). But the experiments were never supposed to work, because success would accelerate the timetable for Colonization, and the experiments were buying time for the Syndicate to develop a “vaccine” to the black oil virus.

Taken as it is, that makes it’s own kind of sense, but it’s clear that the informant is going out of his way to avoid telling the full story. So why is he doing it? Mulder’s explanation for the informant’s behavior works to a certain extent, but that same rationale doesn’t make sense as the episode moves forward.

The informant already knows that Mulder is being protected at the highest levels of the conspiracy, based on his actions in previous episodes. So he knows that Mulder is not going to be killed. So what has changed? And why would the informant push Scully to steal the alien fetus from Fort Marlene, using her own name and basically making it very easy for someone to track her.

The answer, of course, is that it’s a setup. Only it’s the informant that’s being tested here, not Mulder and Scully.

For several episodes, it’s been clear that Mulder and Scully have learned too much, and Mulder’s claims are becoming too credible to be used as effective disinformation. All of this has led the Syndicate to push for the X-Files to be shut down. With the shutdown of Berube’s experiments failing to proceed as planned, the Syndicate has the informant point Mulder in the right direction, so he can take some kind of illegal or non-sanctioned action to find the truth. All the while, he’s also helping the Syndicate track down Secare.

However, there’s a second side to the operation. Given his own sense of desperation, it’s clear that the informant knows that the X-Files are to be shut down. By holding onto Mulder at the end of the operation, they give the informant a chance to show where his loyalties ultimately lie. They keep Scully and the informant under surveillance (which we know from the death of Dr. Carpenter), and then once they know what the informant has offered, replace the actual experimental tissue with one of their decoys (related, no doubt, to the decoy in the fourth season finale “Gethsemane”).

This brings the end of the episode into clear focus. Mulder would have been allowed to live anyway, but now there’s a paper trail showing Scully gaining access to a classified containment facility. The Syndicate would have to know that the informant gave her that access, proving that he’s crossed the line. With the basis for the shutdown of the X-Files and the evidence against the informant confirmed, they let Mulder go and kill the rogue operative.

Other elements of the mythology are introduced here, beyond the intrigues of the conspiracy. One of the more interesting mysteries involves the true nature of “Purity Control”. It’s an odd name for something that would be used in gene therapy. Usually a control sample is meant to represent normal, unchanged conditions. So what is “Purity Control”?

Later seasons reveal that “Purity Control” is the name of the vaccination phase of the project, so named because the vaccination is meant to control the spread of Purity, the supposed name of the intelligent black oil virus. However, it’s very possible that this episode presents two different “Purity Controls”.

The first “Purity Control” is the name of the project in Fort Marlene, which matches the later explanation. But the “Purity Control” in the Erlenmeyer flask may be part of animal experiments conducted as a part of the vaccination project, and not directly related to the hybridization experiments involving Secare. Rather, the agitated and violent animals in Berube’s lab may be intentionally infected with the alien virus, and then used as a control group for the vaccination trials.

The episode implies heavily that there are connections between Secare, the contents of the flask, and the alien fetus. To a certain extent that’s true, but the connection may be less direct than it seems. The contents of the flask are a form of Purity, being used as a control in the vaccination phase. Scully says that the virus is contained within the bacteria to create a kind of gene therapy, which by implication was used to create the hybrids like Secare.

In later episodes, it’s revealed that the effect of the green liquid on humans is due to a retrovirus. There is a similarity in function and behavior between the retrovirus and the black oil virus, with the difference being largely sentience. The “green” form of Purity is non-sentient, and the later “black” forms of Purity have varying degrees of sentience.

But the liquids are simply carriers, so the appearance of the virus within the carrier fluid doesn’t necessarily mean anything. It’s the connection between the two that is key. One form must have somehow given way to the other, either through normal evolutionary patterns or purposeful genetic engineering. Later seasons suggest that the black oil virus is very old, and that it uses the alien Colonist form as a host body, which is gestated within a genetically suitable host animal in and of itself.

So where would the alien fetus have come from? The fetus appears to be Colonist, but they don’t breed. They gestate. The only other explanation is that the Colonists originally did breed, before they became host forms for Purity. If Purity was a natural virus within the Colonist environment, then it could have been in symbiosis with the Colonist species in the retroviral form, and then after gaining sentience, subsumed the Colonists. The fetus would be a holdover from the times when the Colonists bred.

However, since Purity is supposed to have been around for millions of years, that would mean that the alien fetus would have to have been kept in viable stasis for at least that long. While that’s possible, it represents a weak point in the theory.

There are other explanations, based on what has been revealed. Soon after Roswell, the conspiracy was formed in order to use the recovered tissue to produce “super soldiers”, utilizing cloning techniques to develop test populations. If the black oil is an advanced version of the retrovirus, based on their apparent relationship, then could Purity have been genetically engineered from the retrovirus in some way?

This is also supported by the fact that the green liquid that spewed out of Secare wasn’t nearly as potent as the later incarnations of the same “blood”. Mulder survived without the need for any kind of special treatment, after all, and Secare’s ability to heal seemed less advanced than the later hybrids like Cassandra Spender.

However, Secare is similar to the other hybrids in that the man with the crewcut knew to eliminate Secare with a shot to the back of the neck. Given that the shot didn’t cause a complete cellular breakdown, it’s likely that the green liquid in Secare worked as some kind of parallel lymphatic system, with a vital organ at the base of the brain.

This would be very similar to the condition that Emily suffered in the beginning of the fifth season. In her case, however, the experiments seemed to be more advanced, involving direct genetic engineering of the embryo rather than gene therapy of a fully developed adult. But all of these factors suggest once again an emerging genetically engineered pathogen.

This episode doesn’t provide enough information to make the case either way. What this episode does present, however, is the heavily implied link between Purity and the retrovirus found in the green “blood” of alien physiology. Unfortunately, the details of that connection, as shown in later seasons, don’t add up as well as the writers might want to believe.

Memorable Quotes

SCULLY: “Do we even know why the suspect was being chased?”
MULDER: “As far as I can tell, he wouldn’t pull over for a moving violation.”
SCULLY: “Well, that ought to put him in the Ten Most Wanted list…”

MULDER: “You think he does it because he gets off on it?”
SCULLY: “No. I think he does it because you do.”

MULDER: “You know, from day one, this has always been on your terms. I’ve gone along, been the dutiful son. But maybe this time, we can just cut out the Obi-Wan Kenobi crap and you can save me the trouble.”
INFORMANT: “I fear you’ve become too dependent on me.”
MULDER: “Let me tell you something. I’ve got plenty to do without chasing down your vague leads or trying to decode your circular logic. Maybe it’s you who’s become too dependent on me…on my willingness to play your games.”

SCULLY: “OK, Mulder, but I’m warning you…if this is monkey pee, you’re on your own…”

INFORMANT: “Trust…no one…”


- I can’t place the movie that Mulder was “watching”…but isn’t it interesting that it talks about something being hidden inside of a rock?

- As Chris Carter never fails to point out, Gillian Anderson is really starting to show the signs of pregnancy in this episode…

- Why would Mulder fail to recall that no description of the suspect had been released?

- Why were the contents of the Erlenmeyer flask red? I seem to recall another “virus” in the late seasons that were resident in human blood…

- I love the look that Scully gives Mulder when she gets done telling him how absurd he’s being!

- And then there’s that line of Mulder’s about being the “dutiful son”. Another odd coincidence, or actual foreshadowing?

- Secare and Berube are two of the most annoying names to keep track of…way too similar…

- Berube graduated from medical school in 1974, which would have been the perfect time for him to be recruited by the nascent vaccination project begun early that same year.

- The mention of the Human Genome Project connects back to “Eve” and the considerable effort to map human DNA for the purposes of direct genetic engineering…

- I guess Berube didn’t have very observant neighbors, considering how blatant Mulder was about breaking in!

- Speaking of blatant, how could Mulder have missed the man with the crewcut, considering that he was in plain sight?

- Why didn’t Secare realize that he wasn’t talking to Berube?

- Zeus Storage was 1616 Pandora Street. And of course, they play up the idea of Pandora’s Box in this episode…the fact that once the truth is revealed too far, it can never be contained again.

- If Dr. Carpenter knew that Scully understood something of molecular biology, why did she go on to explain the basics of the DNA molecule?

- If it’s not already obvious that Mulder and Scully are being protected, then the fact that Dr. Carpenter was killed and they were allowed to live ought to put all of that into clear perspective!

- Wouldn’t Scully wonder why she was being given access to a restricted facility under her real name? And wouldn’t she have known that signing her name would damn the department?

- For that matter, how the heck did Scully manage to smuggle out the fetus? The answer: she was allowed to take it as part of the plan!

- Why would you use the name of your project as your project password?

- The fact that the informant was the one that they wanted to get the fetus from supports the idea that he was being set up.

- There’s that 11:21 again…

- So are we supposed to believe that the President is part of the conspiracy…or someone in his cabinet?

Overall, this episode is the perfect ending to the first season, introducing mythology elements that would take years to explain and decode. While those explanations never quite added up, that doesn’t take away from the excitement of the convoluted motivations and secrets revealed in this episode. This would begin the storyline that would define the series in the early part of the second season.

I give it a 9/10.

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