“The Beginning” is episode one of season six of The X-Files.
In the season five finale, “The End”, CSM set fire to the X-files, though he took the one on Mulder’s sister, and introduced himself to Spender as the agent’s father. The X-files were closed. The events of The X-Files: Fight the Future took place between that episode and this, though, and Mulder has regained his belief in aliens.
The episode opens in Phoenix, Arizona, with two men running back to a company van having relieved themselves in the desert. In the van another, Sandy, doesn’t look well. He’s dropped off at his house and enters, shivering. He turns the heating up high. Whilst sat on the couch he notices something happening to his hand. The next day the van arrives and a man goes to find Sandy. Sandy is still on the couch, with his chest exploded, as was seen in the film. Whatever came out of him attacks the other man.
Mulder tells a committee that he is piecing together the files and Scully should be able to begin work immediately and explains about the conspiracy to take over the planet with the spacelings, the bees that stung and infected Scully and which cause an E.B.E. to grow inside a human host. Said committee is not impressed. Scully arrives and Mulder says she is there with hard evidence. Except it looks like she isn’t.
Outside. Scully tells him that the virus isn’t what they thought. She can’t identify it, but it’s clearly of Earth. Mulder says it creates an alien being inside a body. Scully tells him it destroys human cells; it creates nothing. She can’t question the science.
In New York, the CSM is filling in the others about the body in Phoenix. Local PD was involved and the deaths made the papers. It’s been blamed on a Native American. Sandy was one of theirs and must have accidentally infected himself and the creature gestated in 12 hours. CSM is told that someone has to find it. He corrects them; someone has to kill it. Yes, he can dispose of the problem.
Mulder is working on piecing the files together when Skinner enters and tells him it’s a waste of time. His reassignment to the X-files has been denied. Unanimously; Skinner voted for it too. Presumably because the conspiracy’s members walk the same halls. He does suggest that Mulder take a look at a file folder on his desk in his old office. The file is there, as is Spender. Spender has been reassigned to the X-files, though he doesn’t believe in them. Another does; Diana Fowley. Evidently recovered from being shot. Mulder leaves, but the file goes with him.
The CSM enters a surgical theatre, smoking. He needs someone bandaged and dressed. That someone is Gibson, and they’re doing brain surgery on him. And the CSM is smoking whilst they do it. Not hygienic.
Mulder and Scully arrive at the house in Phoenix; Scully tells Mulder that what they are doing is a technical violation of state laws before asking herself why she bothers. There are bloody claw marks on the wall, which were apparently caused by the bare hands of the attacker. Scully has found more claw marks on the hardwood flaw and says that did not happen barehanded. Mulder has dug a piece of broken nail out of the marks on the wall. The TODs of both victims were hours apart. Mulder thinks the attacker was celebrating his birthday. Scully can’ see how anything new-born could do this.
Gibson is outside with CSM and a driver. He tells them the alien has left. Clearly, Gibson can sense Mulder and Scully inside, and doesn’t want them found. Inside. Mulder is telling Scully he saw the creatures and she would have seen them too, if she wasn’t infected. Scully explains the science. Mulder says the science is wrong.
At the Rolling Hills nuclear power station outside Phoenix, one man, Homer – no, that name is probably not a coincidence – is sent by another to check out the bleed cooling system. Homer finds something. It does not end well.
Agent Fowley is telling Mulder that she is working on his side, making sure that someone who believes as he does is still working on the X-files. After all, she found them with him. Mulder believes her; Scully is less convinced. Is she trustworthy?