In this episode, Mulder and Scully get told they can no longer work on the X-Files, even though they had been told in the end of the movie that the X-Files was reopened. Diana Fowley (Mulder's old girlfriend) and Agent Spender got to have M&S's old office in the FBI basement. Now Mulder and Scully are working in those little cubicles.
Also in this episode they see more of Gibson Praise (chess kid, mind reader kid). He has his head shaved with all these scars from where the people working for the Cigarette-Smoking Man cut his head open to try to find out what makes him be able to read minds. We find out that alien DNA is active in Gibson's blood, that's how he can communicate with the aliens. It turns out that everyone has some unactive alien DNA in their blood, which is what we call "junk DNA."
The alien (evolved black oil) kills a few people. Mulder theorises that the alien, when it pops out of peoples stomachs, is just a newborn, and is still growing. He's right, and at the end, you see the alien in the nuclear power plant, shedding it's skin and becoming the little alien in "The Erlenmeyer Flask," (Purity Control).
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