Tagline: "Trust No One"
When a man who was a test subject for alien/human hybridization endangers public exposure of these tests, a henchman of the Syndicate ("Crew Cut Man") is sent to terminate the experiments. Mulder, investigating under the indications of Deep Throat, finds himself in the hands of the henchman. Deep Throat has Scully steal what looks like an alien fetus from Fort Marlene to bargain for Mulder's life. Mulder is released, but at the cost of Deep Throat's life. The X-Files are shot down.
and the virus
Dr. Carpenter identifies the
bacteria of the Purity Control flask as alien because it has an extra
pair of nucleotides in its
DNA structure compared to terrestrial DNA, a biology so different from
Earth's that it could have existed on Earth only at its first stages,
when the 4-nucleotide life forms weren't established yet (as Scully
says, "bacteria like this... it may
have existed, but not for millions of years, not since before our
ancestors first crawled out of the sea."). This bacteria contains "something
that looks like
chloroplasts -- plant cells"; this could be the cause for the
of the hybrids' toxic blood.
Inside these bacteria, which are cloned by Dr. Berube, is a virus; of
this virus nothing is told. But as
Scully suggests the bacteria are used to inject the virus into a body
in order to modify the genetic structure of a living being: gene
therapy. And gene therapy is central to all the experiments further in
the series. Only the bacteria are identified as alien, we don't learn
anything of the virus, even if it's this virus which mixes with the
human DNA and not the bacteria's. DT does speak of injecting alien DNA,
so it's obvious this virus is alien, the Black Oil,
Dr. Berube's project is called Purity Control and deals with mixing alien and human DNA through gene therapy. Doing God's work, and what better name for the lab where the experiments took place than Zeus Storage, in Pandora Street? However, Berube wasn't aware he was working for the Syndicate as his surprise at the appearence of the Crew Cut Man indicates ("If you're from the FBI, I've already answered all your questions! [...] Please, my work is very important. I must get on with my work."). Officially, he worked for the Human Genome Project, an (real) ambitious scientific program that worked for "the mapping of all human genes". Being manipulated by the Syndicate that provided him with the Purity Control material, he always thought that his work wasn't alien/human hybridization but a project for the good of science.
Dr. Berube experimented on monkeys, but his work was so successful that he was sure enough to test it on humans. It cured the cancer of his friend Dr. Secare; the other 5 subjects were probably acquaintances too. The water tanks with the hybrid bodies inside will be seen again (2X16: Colony, 4X15: Memento Mori); this seems to be a part of the growing process of a hybrid (be it a clone or issued from gene therapy). But his work was going too fast, and the secret agenda of the Syndicate is not to attain a succssful hybrid too soon (6X11: Two Fathers); hence the Crew Cut Man, who is sent to slow Berube down.
Each group of hybrids we encounter throughout the series is different from one another. With these hybrids are introduced many elements that will be kept as canon, such as the ability to breathe underwater and their green toxic blood. Dr. Secare still bleeds after hiding underwater: these hybrids don't have the ability to heal themselves. Secare is killed from a gunshot wound to the base of the neck, no stiletto is needed here: these hybrids are still quite imperfect.
Deep Throat's demise
Deep Throat says this was the "first DNA transplant, the first human/alien hybrid"; we know this to be somewhat false (2X25: Anasazi). DT means this was the first time the experiments were so successful, because they definitely are an improvement: the hybrids can survive, they have human physiology and can live normal lives without drawbacks (3X01: The Blessing Way, 3X10: 731), they are very close to a successful hybrid. Or maybe this was the first time this technique was used: DT explains we didn't have the technology to make gene therapy up until then, previous experiments were either unsuccessful (The Blessing Way) or didn't consist of gene therapy (the cloned hybrids). It is very likely that DT has been deceived and that his information is false. This episode tells of the demise of DT, he could have purposely been lied to in order to isolate him; his loyalty is in doubt since 1X09: Fallen Angel and he's being watched since 1X16: E.B.E.. DT does say "There are limits to my knowledge, Mr. Mulder.", and his knowledge on hybridization experiments seems very limited.
In the final scene, mirroring the final scene of 1X79: Pilot, CSM disposes of the alien fetus in a cardboard box as if it were no more important than one of hundred nasal implants. DT was certain he sent Scully to fetch the original priceless fetus, in order to have leverge over the Syndicate because of its uniqueness. 6X12: One Son establishes that the fetus really does exist and is of great value; it is indeed stored in Fort Marlene, in those same liquid nitrogen tanks. So Scully didn't get the 'good' authentic one, and the Syndicate only pretended to bargain with DT; their only goal was to make DT come to them and get him eliminated ("I made the deal, Scully, they're expecting me!"). The real fetus must be stored in the same room with the fake one Scully got, in an adjacent tank. But because of its importance, its real location is known only to the few highest-ranking members of the Syndicate; other people, like Deep Throat, are given the false location. Or it could be that the Syndicate anticipated Deep Throat's actions and had the fetus replaced when Mulder was noticed near Zeus Storage.
However, at the end of the episode it is revealed that the fetus is fake and not important for the CSM. It could be a kind of chimera developed by DARPA and Roush (see 5X02: Redux). At the end of season 1, nothing is certain yet, and this whole alien business could very well be nothing but a veil of lies covering the truth that seems to be held not even by Deep Throat but only by CSM.
Deep Throat says "we've had the [alien] tissue since 1947", referring to Roswell. Later he says "the wellspring, Miss Scully, the original tissue" when he speaks of the fetus. From 6X12: One Son we know the fetus was given in 1973, the tissue they've been using up until then was from bodies of aliens from downed UFOs. What DT means is that though they've had alien tissue in their possession since 1947, the tissue used as raw material from 1973 and on is the fetus. Dr. Berube was cloning the original cells to have more material to work on ("Some kind of bacteria, each containing virus and it looks as if Berube may have been cloning them.")
Deep Throat tells Scully "In 1987, a group of children from a southern state were given what their parents thought was a routine inoculation. What they were injected with was a clone DNA from the [fetus] as a test." This is the exact case profile for 2X10: Red Museum, where we encounter again DT's murderer, the Crew Cut Man.
Title note: An Erlenmeyer flask is a common object in chemistry labs. The flask containing "monkey pee" (labelled "Purity Control") is an Erlenmeyer flask.
"Purity Control" -the name of the program involoving alien/human hybridization and the password to access the alien fetus in Fort Marlene.
Scully: "Who is this Deep Throat character? I mean, we don't know anything about him. What his name is, what he does..."
Mulder: "He's in a delicate position. He has access to information and indiscretion could expose him."
Scully: "You don't know that this isn't just a game with him. He's toying with you. Rationing out the facts."
Mulder: "You think he does it because he gets off on it?"
Scully: "No. I think he does it because you do."
Deep Throat: "Under the circumstances, I've given you all I can."
Mulder: "A news report?"
Deep Throat: "And where has it led you?"
Mulder: "Not very far."
Deep Throat: "It may be further than you realized."
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."
Deep Throat: "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." (starts to walk away)
Deep Throat: "Mister Mulder?"
Mulder: "Closer to what?" (Deep Throat sighs and walks away)
Scully: "You know, I've always held science as sacred. I've, I've always put my trust in the accepted facts. And what I saw last night... for the first time in my life, I don't know what to believe."
Mulder: "Well, whatever it is you do believe, Scully, when you walk into that room, nothing sacred will hold."
Scully: "I don't trust you!"
Deep Throat: "You've got no one else to trust!"
"Trust...no one." -Deep Throat's last words