The Beginning is the first episode of the sixth season of the X Files. Just after having returned from Antarctica, Mulder and Scully conduct an unofficial search for a vicious alien in Phoenix, Arizona.
He enters and turns the thermostat up as high as possible. He appears to be freezing cold and looks at his hand to see that it is becoming translucent.
His coworker comes to pick him up the following morning, but he doesn't answer the door. The windows are condensated and the house is very humid. His friend enters the house and finds Sandy on the couch. His stomach appears to have burst open. The man is then viciously attacked by a grotesque, long-clawed alien. He attempts to open the door but is dragged back inside and clawed to death.Mulder is trying to enhance a portion of a burned X-file in his basement office and, later, he explains to an OPR panel that he believes a lot of the files that were burned in his office will be salvageable. Mulder continues to recount what happened to himself and Scully in Antarctica and outlines an elaborate scheme, involving a shadow group within the government that is growing corn which contains genetically-engineered pollen to hold a virus that will be taken away by bees. According to Mulder, the bees will transfer the virus through their stings, which will trigger the growth of an extraterrestrial being within a human host. He tells the panel that Scully has proof of these bees but, when given the opportunity to corroborate his account, she does not support his statement.
After the review, Scully tells Mulder that the virus is not what he thinks it is, stating that the virus is very much of this world.In a shadowy meeting, the secretive Syndicate conclude that it took only twelve hours for the alien to gestate and the Cigarette Smoking Man says that they must kill the being, whatever the cost.
Meanwhile, Assistant Director Skinner tells Mulder that his request to be reassigned to the X-files has been denied. Skinner says that he might be able to help Mulder obtain proof of what he is alleging and hands him a folder that contains a disturbing picture of the man who was killed in Arizona.
In a surgical operation room, the CSM supervises a procedure on Gibson Praise's brain but tells the medical staff to conclude the operation because Gibson's expertise is required.
At the crime scene in Arizona, Mulder describes to Scully what happened to the man. He says that the first man was killed hours before the second. He then says that the same thing happened to a man he had seen in Antarctica. Mulder also finds what appears to be a fingernail embedded in a claw mark on one of the walls.
The CSM pulls up to the house with Gibson, who tells him that the creature is no longer in the house.
A man named Homer is sleeping at his work station at the Rolling Hills Nuclear Power Plant, outside Phoenix. A co-worker wakes him up and reminds him that he should be doing his routine systems check. While checking, the co-worker notices that the cooling system is overheating. Homer consequently goes into the plant, to investigate. The alien grabs and kills him.Mulder and Scully arrive at the plant. Special Agent Jeffrey Spender is already there and tells Mulder to leave. Mulder and Scully go back to their car, where they find an unconscious Gibson in the vehicle's back seat.
Scully nurses him back and she sees what they did to him. The incisions on his head were poorly sutured. He tells them that he got away from his captors and went to them for refuge. He has infections and a fever. Scully recommends that they take him to a hospital.
Just as Scully and Mulder are driving Gibson to the hospital, Agent Diana Fowley arrives and stops them, but she doesn't see Gibson. She tells Mulder that she is on his side but has to pretend that she isn’t. Mulder reluctantly trusts her and they go to the power plant. Scully takes Gibson to the hospital.
Fowley tells Mulder what happened. She suggests that the alien entity is still developing and that is why it went to the power plant, to get heat. They enter the power plant and look around. Near the place where Homer was killed, Mulder finds what appears to be the skin of an alien as if it had molted. Mulder gets a call from Scully and she tells him that Gibson has been infected with the virus.
As she is calling Mulder, a Syndicate operative dressed as a hospital worker kidnaps Gibson from the hospital and takes him to the power plant, so he can find the alien. Mulder witnesses this happening through a locked door with a window. Just as this happens, the man is attacked by the alien. After killing the man, the alien looks at Gibson. Mulder calls out to Gibson, but can’t get to him. Agent Fowley returns and draws her gun on Mulder as power plant security officers arrive.
In Mulder's old office, the CSM is talking to Spender and tells him that he did well. Spender says that there is no way that Mulder will give up. The CSM says that there are solutions but that they can’t use them, in this scenario. The CSM says that you can kill a man but you can’t kill what he stands for, unless you break his spirit first.Mulder is reconstructing old X-files documents. Mulder tells Scully that he’s starting to trust Fowley again. Scully says that the DNA from the fingernail is the same as from the virus and that it matches some of the remnant DNA in human bodies. This would mean that all humans are partially alien.
Gibson is hiding back in the plant and is looking over a pool of water with cooling rods. In the water, the alien is molting again. When it completes its molt, it takes the shape of the traditional Grey Alien.
- Roush Technologies is also mentioned in "Redux", in which it is said to not only have bankrolled Kritschgau and Blevins but is also involved in congressional lobbying, in regards to bio-tech issues.
- The sleeping nuclear power plant employee by the name of "Homer" is a reference to Homer Simpson of The Simpsons.
- This episode marks the first appearance of AD Kersh, played by James Pickens Jr.
- 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 caused the generators to be put online. Thus, most scenes in the power plant had to be shot amidst noise higher than 100 decibels. Most of the actors' dialogue had to be re-recorded in the studio.
- The scenes in the nuclear power plant were shot during an intense heat wave. During most scenes the temperature rose well above 100 degrees Fahrenheit.
- From this episode on, 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".
- The film critic Janet Maslin had given The X Files movie a negative review, in this episode Wendie Malick plays an FBI Assistant Director named J. Maslin.
- As the Black-Haired Man is leading Gibson Praise into the power plant, Gibson proclaims "He's here.." When The Black-Haired Man asks "Where?", Gibson's reply is simply "Somewhere..." This exchange of dialog, and also the scene and lighting in which they take place are almost identical to a scene from the Red Dwarf season 3 episode "Polymorph", as Rimmer, Kryten, and the Cat descend into the cargo deck to search for their own "monster of the week".
- The opening teaser is stated as taking place in Phoenix, Arizona, but this cannot be since there are few Joshua Trees in the Phoenix area, certainly not the concentration of Joshua Trees seen as the van drives down the desert highway. This scene appears to have actually been filmed near Palm Springs or even Joshua Tree National Park in California's Mojave Desert.
- William B. Davis as Cigarette Smoking Man
- Chris Owens as Jeffrey Spender
- Mitch Pileggi as Assistant Director Walter Skinner
Special Guest Starring
- Jeff Gulka as Gibson Praise
- James Pickens, Jr. as Assistant Director Alvin Kersh
- Christopher Neiman as First Carpool Man
- Kim Robillard as Homer
- Arthur Taxier as Assistant Director P. Bart
- Alan Henry Brown as Second Carpool Man
- Scott Eberlein as Black-Haired Man
- Wendie Malick as Assistant Director J. Maslin
- Don S. Williams as First Elder
- George Murdock as Second Elder
- Rick Millikan as Sandy
- Wayne Thomas Yorke as First Workman
- Wayne Alexander as Assistant Director G. Arnold
- Ralph Meyering, Jr. as Surgeon
- Benito Martinez as Orderly