“The Erlenmeyer Flask” is episode twenty-four of season one of The X-Files and the season finale.
The episode opens with a car being pursued by a police car. It enters into a shipyard and the fleeing car comes to a dead end. The driver gets out and tries to run for it, but is grabbed by the two officers from the police car. They start hitting him with their batons – then, as a second police car arrives, the fugitive grabs a baton, takes down the initial two cops and a third from the second car. The fourth officer shoots the man with a taser. To absolutely no effect. As the man runs up a conveyor leading over the water, the cop shoots him and the man runs off the end of the conveyor into the water. The officer says he knows he hit the man, and asks where he went because he must be bleeding bad. On the end of the conveyor are several puddles of green liquid.
Mulder is at home asleep with the television on when the phone rings and Deep Throat asks him if he’s watching Channel 8. Mulder switches channel, which is a news report on the chase. He starts taping it as the reporter interviews the local police captain.
Mulder is repeatedly watching the recording with Scully, and making several print outs from the tape. He doesn’t know what he is hoping to find. Apparently, the man wouldn’t pull over for a moving violation. Scully asks how he knows Deep Throat isn’t lying as, by Deep Throat’s own admission in “E.B.E.”, he has lied to Mulder before. Mulder doesn’t believe that is the case here.
They head to speak to the police captain, who says there were several agencies there last night. Mulder asks about a man in one of the images he has printed out, who isn’t wearing a badge or a uniform. The captain doesn’t know who it is. Even though it’s now 18 hours since the fugitive went into the water and the body has yet to be found, the captain is sure it will be. Mulder claims the FBI’s interest is that the suspect matches the description of a federal fugitive. It seems that no description of the suspect has gone out. Mulder then asks about the car; it’s in impound.
The car apparently came from a rental agency who had no idea it was missing. Mulder is looking at the print outs; you can’t make out the car’s license plate. Then he notices something. The car in the photo has a sticker on the windscreen. This car doesn’t. It isn’t the same car.
The symbol, Scully explains, is a caduceus, the adopted symbol of the medical profession. She would know. Mulder has a partial of the real car’s number plate and manages to track it down from these two items. This leads to Emgen Corporation in Gaithersburg, Maryland. A doctor, Berube, is working in a lab when Mulder and Scully arrive. He wasn’t aware his car was missing. He’s also not willing to cooperate much, if he isn’t under suspicion. Scully wants to give up.
As Mulder arrives home that night, Deep Throat approaches him. He is disappointed that Mulder’s level of commitment seems to have diminished. Mulder wants more; Deep Throat has given all he can. Mulder shouldn’t give up; he’s never been closer.
Dr Berube is still in his lab when the unidentified man from the scene arrives. The man says that he’s alive – presumably meaning the fugitive – and wants to know if Berube has been in contact with him. The man wants to know about the questions the FBI asked and where the fugitive, Dr Secare, is. Berube wants to get on with his work. He’s told his work is done. Out in the harbour, the police captain calls off the search. And Dr Secare emerges from the water as the boat leaves.
Dr Berube is dead, listed as a suicide. He went out of a window, but first trashed his lab and tied one end of a roll of medical gauze around his neck and the other around a gas outlet. Mulder thinks that is odd and Scully agrees. It’s as if someone wanted to ensure the doctor broke his neck before he hit the ground. They can’t fit the pieces together, but Mulder finds an Erlenmeyer flask labelled ‘Purity Control’ and asks Scully to investigate it as Mulder investigates Berube.
At the microbiology lab at Georgetown University, Scully isn’t expecting much from the sample, which is a bacterium. However, she’s told she has definitely got something. Bacteria, but not one the woman examining it has ever seen. It’s strange.
Mulder is making a call from inside Berube’s house to track down a phone number as Berube’s killer arrives in a van with a parabolic mike. Then Dr Secare phones and Mulder tries to arrange a meeting. However, he’s badly injured and collapses, and someone calls an ambulance for Secare. In the ambulance, a paramedic is following instructions over the phone but, when Secare’s chest is punctured, gas is emitted and everyone else in the ambulance clutches their eyes as the driver stops it.
Scully’s bacteria contains a virus and apparently plant cells. The only reason for this is to inject it into someone living, gene therapy. The bacteria is ancient, too. Mulder stumbles across a secret lab with people in tanks. The virus in the bacteria seems to contain extra-terrestrial DNA. And whoever is behind this is lethally cleaning things up.
At the end of the opening credits, for the first time ‘The Truth is Out There’ is changed. To ‘Trust No One’.