S3E1 · The Blessing Way

In Two Grey Hills, New Mexico, Albert Hosteen (Floyd Red Crow Westerman) and his family are beaten by the Men in Black as they search for the whereabouts of Fox Mulder (David Duchovny). Dana Scully (Gillian Anderson) is pursued by a black helicopter before soldiers retrieve her printed copies of Albert's translations of the digital tape, but they cannot find the original. Scully denies having the original tape, saying it is in Mulder's possession. Upon returning to Washington, the FBI puts Scully on mandatory leave and forces her to turn in her badge and gun. Upon entering Mulder's office, she finds the tape missing.

Meanwhile, in New York City, The Smoking Man (William B. Davis) appears before the Syndicate, who question him over the whereabouts of the tape. Mulder, alive but severely wounded, is found buried under some rocks near the buried boxcar. Hosteen has Mulder taken to a Navajo sweat lodge to be healed during a "Blessing Way" ritual. During the ritual, Mulder has ghostly visions of Deep Throat and his father, who urge him to recover and continue his search for the truth.

Melvin Frohike visits Scully's apartment and shows her a newspaper article about Kenneth Soona's murder. When she returns to FBI headquarters, the metal detector curiously goes off. Scully presents Skinner with the newspaper article, thinking that the data from Soona's death can clear Mulder in his father's murder. Skinner, however, refuses to do any follow-up on it. After Scully leaves, it is revealed that the Smoking Man was waiting in an adjacent room to question Skinner about the exchange. Leaving the building, Scully has a hunch upon seeing the metal detector again that leads to locating metal in the back of her neck. Scully sees a doctor, who removes a small metal implant.

Scully's sister Melissa urges her to see a hypnotherapist to recover lost memories of her abduction. Scully does so, but becomes scared and stops the session. Returning home, she finds Skinner leaving her apartment; he later denies being there. Mulder, recovered from the ritual, is told by Hosteen that he cannot bathe or change clothes for four days. Scully attends Bill's funeral in Boston, where she introduces herself to Mulder's mother, Teena. At the cemetery, Scully is approached by a Syndicate member known as the Well-Manicured Man, who warns her that she is about to be killed, either by a pair of assassins or by someone she knows. Mulder goes to Massachusetts and questions Teena about an old photo of his father standing with the other members of the Syndicate in front of a mysterious building.

Melissa calls Scully and tells her she is coming over. After receiving a call from someone who immediately hangs up, Scully leaves her apartment and tells Melissa that she'll head to her home instead. As she leaves, Skinner pulls up in his car, telling her they need to speak in private. Melissa shows up soon afterwards and is mistakenly shot by Luis Cardinal, who is hiding there with Alex Krycek. Realizing they shot the wrong person, the two flee. Meanwhile, after taking Skinner to Mulder's apartment, Scully holds him at gunpoint, believing he is the traitor the Well-Manicured Man spoke of. Skinner tells Scully that he is in possession of the digital tape. Just then, someone steps outside the door. This distracts Scully enough for Skinner to pull his gun on her.