Directed by: Kim Manners
Mulder and Scully are brought before a review board to justify their re-assignment on the X-Files. The board needs scientific proof of extraterrestrial life. Mulder argues that concrete evidence exists via Scully, who had earlier been infected by an alien virus. When Scully is vague regarding this infection, the board gives the team their final warning - find concrete evidence or else.
On the sly, A.D. Skinner gives Mulder a lead on a strange case in Arizona that might give him the hard evidence he needs. At the crime scene, Mulder theorizes that the victim was infected by an alien virus and that this virus ultimately produced an alien entity. The entity then ripped away the victim's chest from the inside as it birthed itself. Meantime, the Syndicate is irate that this "situation" has surfaced and is getting so much attention. Cigarette-Smoking Man assures them that he is taking care of the problem. He brings Gibson Praise, the young chess prodigy, to the crime scene in hopes that Praise can divine where the creature has escaped to.
The agents are drawn to a nearby power plant where another murder has occurred. They are met by agents Spender and Fowley who deny Mulder access to the new crime scene. When Mulder and Scully return to their car, they find Praise hiding in the back seat.
Mulder wants to use Praise to find the alien creature, but Scully talks him out of it, explaining that Praise is the scientific evidence Mulder's been looking for. Praise can corroborate everything Mulder's been saying. Scully tells Mulder that Praise needs medical attention and just as they're about to drive him to the hospital, Agent Fowley arrives. Scully continues on to the hospital with Praise, while Mulder and Fowley go to the plant to find the creature.
At the plant, Mulder and Fowley discover evidence that the alien is there. He calls Scully at the hospital to tell her this; in turn, she reveals that Praise has traces of the alien virus in his body - somehow, Praise is part extraterrestrial. While Scully's attention is diverted, Black-Haired Man kidnaps Praise and takes him to the power plant to find and destroy the alien. Mulder catches up with Praise and Black-Haired Man, but it is too late. They have locked themselves inside the core reactor room. Mulder watches helplessly as the alien kills Black-Haired Man. The alien turns on Praise just as the plant's alarms sound and FBI agents swarm the area. Fowley, now seeming to be on Spender's side, approaches Mulder and tells him to back off.
Back at the review board, the panel tells Mulder and Scully to cease all association with the X-Files. They are put on probation and told to report to a new boss, Assistant Director Kersh.
The part of Sandy, the Syndicate scientist who unwittingly incubates an alien inside him, was played by longtime X-Files casting director Rick Millikan.
The nuclear power plant was actually a conventional generating facility that ran only rarely at times of extreme power demand. The heat wave that hit Southern California during the filming made that the generators had to be put online. Thus most scenes in the power plant had to be shot amidst noise higher than 100 decibels. Most of the actor's dialogue had to be re-recorded in the studio.
From this episode Chris Owens is now billed under the "Also Starring" heading.
"Homer", sleeping at the helm of the nuclear power plant, was a nod to The Simpsons dad, Homer Simpson; a show which portrayed Mulder and Scully in cartoon form in the episode "The Springfield Files".
In an interview with the LA Times (August 28, 1998), Chris Carter explained that the first thing in the opening teaser of the premiere is a shot of the sun. The camera then pans down to a desert landscape - a scene they would never have been able to do in Vancouver. Carter says that these opening images are a "wink to the audience that we are now in the land of sunshine".
Scully: Mulder, let me remind you once again... What I saw was very little.
Mulder: Look, Scully, that excuse is not going to work this time. You were there and you were infected with that virus.
Scully: Mulder, yes there is a scientific basis for what happenedto me. I was exposed to a virus but as it turns out, Mulder, that virus is not what you thought. Look, I can't identify it, Mulder... I have runthree separate tests - but I can tell you without a doubt that that virus' DNA and proteins are very much of this world.
Mulder: I saw what that virus did. I saw it generate a new being... An alien being inside a human body.
Scully: It attacks and destroys human cells but that is all it does,Mulder. It creates nothing. Look, I don't like telling you this... And Iknow that you don't want to hear it... Not that you can't question meand what I saw but what you can't question is the science.
Skinner: You're wasting your time.
Mulder: You need evidence to justify our reassignment.I've just got to bring it back from the ashes.
Skinner: Nothing you might restore is going to help you, Agent Mulder.It's over and done. Your reassignment on the X-Files has been denied.
Mulder: (angry) How can it be denied? We're the only reason the X-Files were reopened in the first place. There's no other reason to reopen them.
Skinner: I'm not arguing...
Mulder: Well, then, who is?
Skinner: When will you accept that no amount of pressure or reason will bring to heel a conspiracy whose members walk these halls with absolute impunity?
Mulder: Was there a vote?
Skinner: Unanimous against.
Mulder: I don't see there's any argument here. You admit yourself that the crime report is a lie.
Scully: Mulder, that doesn't mean that I can just accept your theory.
Mulder: What does it take? For this thing to come up and bite you on the ass?
Gibson: It's not here. Why don't you believe me when you're so afraid of me?
CSM: I'm not afraid of you.
Gibson: You think I can destroy you for what I know, because of what I am. You're thinking you could've destroyed me, too and if I don't find this creature, you will.
A clip from ''The Beginning''
Episode Number: 118
Season Number: 6
First Aired: Sunday, November 8, 1998
Production Code: 6X01