Daylight. The episode opens on a group of military police surrounding a house. They take down the door, spreading out through the house. Looks of shock appear on their faces as they find a man, shaking and covered in burns, huddled in a corner. He’s going to need a doctor.
Scully sits at a bar, wearing some terrible 90s eyeglasses and flipping through notes. Mulder appears and it almost looks like he’s going in for a kiss, which is a little weird. He stops short and offers to buy her a drink. Scully, ever the professional, refuses to drink at 2pm. Mulder goes on to tell her about a military pilot of experimental aircraft who had a psychotic breakdown, was taken in for hospitalization and hasn’t been heard from in 4 months. I love the sly amusement in Scully’s face and voice whenever she questions what Mulder is telling her. She clearly thinks he’s nuts.
This is the episode in which we first meet Deep Throat (kinda obvious from the title), the man who will become the agents’ contact and giver of sometimes reliable information, who warns Mulder off the case. This is the first episode that really opens up the X-Files mythology. Conspiracy is afoot and Mulder’s interest in this case gets rewarded by someone having his phone tapped.
No one wants to talk to anyone. That seems to be a theme of this episode. Military refuse to talk to Mulder and Scully about the missing pilot. Another pilot’s wife refuses to say anything about the military, and admonishes the wife of the missing pilot for bringing in outside forces. It’s the ‘ufo nuts’ who end up being the source of the best (and only) information, directing the agents to Ellens Air Force base.
This episode is full of UFOs, which Mulder thinks have been created by reverse-engineering alien technology. When nearing the air force base at night, Mulder and Scully see two points of light in the sky, moving in ways aircraft couldn’t possibly maneuver. They also find a couple stoners, one of which is a very young Seth Green, who end up providing more information than anyone.
Besides possible alien technology, this episode introduces the idea that the military is able to wipe people’s memories or re-wire their brains. The missing pilot comes home but his wife calls the agents for help, insisting that this man isn’t really her husband. He doesn’t know things he should know, and he doesn’t remember where he’s been for the last months. After this, the chilly reception the agents received from the military gets downright hostile, as men in black accost them, destroying photographs they had taken and telling them to gtfo.
Mulder doesn’t like being told what to do so he lies to Scully and runs off to explore the air base in secret. Good move, hot shot. He sees a UFO (not necessarily alien, but definitely unidentifiable) up close and then is immediately captured, strapped to a gurney, and injected with drugs, while Scully has to go rescue him. It’s actually a nice reversal of what tends to happen in future episodes. Scully gets captured a lot in the coming seasons. Scully lays the smack down (shut up, it’s the 90s) on airforce security personnel, holds him at gunpoint, and demands he bring her to the base to find Mulder. Before they can get into the base, Mulder is sent out, looking like a lost, drugged up puppy. He doesn’t remember anything.
You’d think being federal agents would afford Scully and Mulder some degree of safety or respect but this episode makes it clear that if they keep pursuing the alien / government conspiracy thing, they will never be safe. At least Mulder gets thrown a bone at the end when Deep Throat visits him and confirms that “they (aliens) have been here for a long, long time.”