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The Erlenmeyer Flask
Directed by R. W. Goodwin
Dr. Carpenter: A fifth and sixth DNA nucleotide. A new base pair. Agent Scully, what you are looking at... it exists nowhere in nature. It would have to be, by definition... extraterrestrial.
A car chase in Maryland ends with the fugitive overpowering several officers, bleeding green blood, and disappearing into the water. When Deep Throat points Mulder to the case, he and Scully find themselves investigating. Scully doesn't trust Deep Throat, but both she and Mulder find themselves led to a gene therapy experiment of possibly extraterrestrial origin, as well as government spooks looking to cover it up at any cost.
- The Adjectival Man: One of the men in black is known only as Crew-cut Man.
- Alien Blood: The participants in the gene therapy experiment developed green blood that emits vapors that are toxic to non-hybrids.
- Anyone Can Die: Mulder's Mysterious Informant Deep Throat is killed at the end of the episode.
- Artistic License – Biology: Scully describes chloroplasts as plant cells; a chloroplast is in fact an organelle, a specialised structure within the cell. To use an analogy, she called your liver a person.
- Book Ends: The first and last episodes of the season end with Scully lying awake in bed at 11:21 pm in blue pyjamas and getting a call from Mulder with bad news, right before the Cigarette-Smoking Man places an alien item into a secure storage facility in the Pentagon.
- Captain Obvious: A microbiology expert explains the rudiments of genetics — material taught in any high school's freshman biology class — to Agent Scully, a fully qualified doctor.
- Coincidental Broadcast: Mulder watches the news informing on the case he's about to investigate. Justified because Deep Throat, his secret informant, called him to tell him to watch it.
- The Conspiracy: As exposited by Deep Throat; this time we learn US Intelligence has "black groups", one of which has been wiping out the evidence (and people) of the Purity Control project.
- Destination Defenestration: One of the murder victims was chucked out of his lab window.
- Downer Ending: Mulder is released by the MIB, but Deep Throat dies in the process, the X-Files are shut down, and both agents are re-assigned.
- Half-Human Hybrid: Terminal patients were given gene therapy with alien DNA, which on top of curing them also gave them super strength, toxic green blood, and the ability to breathe water. Handy.
- Heroic Sacrifice: Deep Throat outs himself as the traitor within The Syndicate to save Mulder's life, almost certainly knowing what the price was going to be.
- It Was Here, I Swear!: When Mulder returns to the storage unit full of incubating hybrids, it's been entirely cleared out.
- Killed Off for Real: Some people on this show were only seemingly dead or even managed to get resurrected. Not Deep Throat. He was offed for good, never to return but in hallucinations, flashbacks, or alternative realities.
- Meaningful Name: Zeus Storage on Pandora Street is named after Pandora's Box. Probably not a good idea to open that door.
- Myth Arc: It was a mythology episode, as is becoming for a Season Finale.
- No Escape but Down: A fugitive flings himself off the jetty and into the sea, and disappears.
- Not of This Earth: Just look at the page quote.
- People Jars: In Zeus Storage there are five glass tanks similar to aquariums with naked men, alive and breathing underwater. But they're not entirely human."You're standing in the room where the first DNA transplant took, the first human-alien hybrid was created."
- Person as Verb: Person from popular culture as adjective. Mulder gets angry with Deep Throat.Mulder: But maybe this time, we can just cut out the Obi-Wan Kenobi crap and you can save me the trouble.
- Ripped from the Headlines: The ambulance scene is based on the contemporaneous Gloria Ramirez incident.
- Super Not-Drowning Skills: One guy from the experiment hid under water for three whole days. Justified, since one of the effects of the experiment is that he can breathe underwater.
- Virus and Cure Names: The episode introduces the infectious, alien form Purity, also known as black oil. The same episode gives a putative name —Purity Control— to the vaccine that wouldn't be developed until several episodes later.
- Wham Episode: And how, as it set the wham standard for all subsequent season finales. We see the first alien-human hybrid, Scully receives near-indisputable evidence of extra-terrestrial life, Deep Throat is shot dead, and the X-Files unit is shut down.
- Wham Line: Thirteen days after Deep Throat's death, Dana wakes up to a phone call by Mulder, who tells her some distressing news:"They're shutting us down, Scully."
- Wham Shot: Literally. Dana witnesses Deep Throat handing over a box containing the alien fetus to the Crew Cut Man. He heads to his van to put the box inside, walks up to Deep Throat... and immediately shoots him in the chest.