S6E1 · The Beginning

In Phoenix, Arizona, a scientist working for Roush Technologies is exposed to the black oil; an alien creature gestates and bursts from his body the next morning. A few hours after his death, a co-worker who arrives at his house is attacked and killed by the newborn alien.

In Washington, D.C., Agent Fox Mulder appears before an FBI panel regarding his experiences in Antarctica. Meanwhile, the Smoking Man (William B. Davis) reports to the Syndicate on the alien in Phoenix, confident that he'll be able to kill it. Assistant Director Walter Skinner tells Mulder, who is working on restoring the burned X-Files, that he and Scully have been denied reassignment on the unit, but that Mulder should seek out a folder left on the desk in his old office. Mulder goes there, only to discover that Jeffrey Spender and Diana Fowley have been assigned to the X-files. Feeling betrayed by Fowley, Mulder leaves, but not before stealthily taking the folder with him.

The Smoking Man seeks Gibson Praise, who is undergoing brain surgery at that very moment. Mulder and Scully head to the home where the alien gestated, finding an alien's nail in the wall. The Smoking Man arrives soon after with Gibson, who tells him that the alien is no longer there. At a nuclear power plant, the alien kills another person, but Mulder and Scully are denied access by Spender and Fowley. Upon returning to their car, they find a hiding Gibson, having escaped from the Smoking Man. Later that night, Fowley tells Mulder she was offered the X-files and is protecting his interests. Mulder leaves Gibson with Scully and heads off with her. Mulder and Fowley believe the alien is seeking heat, which is why it is at the power plant. Inside, they find organic material on the ground and cooling pipes.

Scully brings Gibson to a hospital, where it is determined that he has the alien virus in his blood. The Black-Haired Man (Scott Eberlein) kidnaps him soon after and brings him to the power plant. They find the alien, who attacks the Black-Haired Man but not Gibson, as witnessed by Mulder from outside a locked door. Afterward, Mulder and Scully are ordered to not associate with the X-files and are reassigned under Assistant Director Alvin Kersh. Spender is visited by the Smoking Man in his office. Mulder continues to work on restoring the X-Files and is told by Scully that Fowley's report does not reflect what really happened.

She reveals that the alien virus DNA is also part of all human DNA, but in Gibson, the DNA is active. Meanwhile, at the power plant, Gibson is trapped inside with the alien, which sheds its skin inside a spent fuel pool, revealing the traditional grey alien form.