“The Blessing Way” is episode one of season three of The X-Files.
At the end of the season two finale, “Anasazi”, the Smoking Man had the troops with him bomb the buried train carriage containing the dead humans with alien appearance that Mulder had found, and had been in the last time he was seen. Although Mulder was apparently not there according to the soldiers.
This episode opens with flames rising from the opening in the car as the former Codetalker, Albert Hosteen, is saying about how things live as long as the last person who can remember them. That memory is valued over history as history serves those who seek to control it. They seek to extinguish the dangerous fire of truth, but such men are both dangerous and unwise.
The Smoking Man and his soldiers burst into the Hosteen house looking for Mulder. Albert’s grandson is also there, and he has been beaten. The Smoking Man wants Mulder and the files. He seems upset and not in control for once. Albert tells him that he will find nothing. Scully arrives after the Smoking Man has gone. The place has been turned over and she’s told they were looking for Mulder. Scully wants to know where he is and Albert’s grandson takes her to the still-smoking train car. That night, as Scully is leaving the Navajo Reservation, a light from behind turns into a helicopter than lands in front of her. Armed soldiers and the Smoking Man get out. He wants the files. Scully has them in the car’s boot, but not the DAT. Mulder has that. The files are taken and they leave.
In Skinner’s office, Scully is being told by others that it is the recommendation from the Office of Personal Conduct that she takes a mandatory leave of absence without pay or benefits. She will leave her weapon and badge but will remain available to answer further questions regarding the investigation into Mulder’s whereabouts. As far as Scully knows, he’s dead.
Outside the office, Skinner tells Scully that those people have a protocol to follow. Scully asks about the protocol regarding Mulder being poisoned – she discovered LSD was being put into his apartment building’s water. That the people who did that killed Mulder and his father – Krycek having killed the elder Mulder. Skinner reassures her they will be found. She doubts that. She heads to Mulder’s office looking for the DAT, but it’s gone.
The Smoking Man is at a meeting with others. He is reassuring them that the files are recovered – he’s not telling the full truth – and that those involved in the theft have been removed. The FBI matter will be handled internally. The sole media attention will be a few scattered obituaries. Mulder is dead and his body will not be recovered.
On the reservation, Albert narrates again. Some boys have seen buzzards circling, and such birds are found where something has died or is nearly dead. A party heads out and finds a hand under a pile of rocks, with Mulder underneath, near death. The Navajo are going to hold a Blessing Way chant as only the Holy People can save Mulder’s life now.
A rather drunk Frohike comes to see Scully. He asks if she’s going to take up the torch. She says she can’t; she’s out. Frohike has a news article, regarding the death of Kenneth Soona. Frohike explains to Scully who he was. Soona was killed execution-style, but after Mulder had disappeared. Scully has an idea; she wonders if they could have been so stupid.
Albert is holding the ceremony, but is concerned that Mulder may not want to return; he may want to be with his father. Mulder seems to be having visions during this, of Deep Throat and his father, talking to him and telling him to go back and live. William Mulder says he was ashamed of the choices he made when Mulder was a boy.
Scully has returned to the FBI, but not as an agent. She sets off the metal detector on entering, and is scanned more closely, but nothing. Neither she nor the guard know why it went off. Scully has come to show Skinner the news article. She wants ballistics running against the bullet that killed Mulder’s father, as it would prove that Mulder didn’t kill him. Skinner tells her that ballistics would have already been entered in the system, and a connection would have been made if there was one. He also mentions that he has been asked to execute a search warrant on Scully’s apartment, looking for the tape. It’s the smoking gun; bring him the DAT. Scully says she doesn’t have it and Skinner tells the Smoking Man after she leaves that he thinks she’s telling the truth. The Smoking Man thinks that’s unfortunate.
Scully also checks again on the way out to find out why she set off the metal detector. Which causes her to poke deeper. Her sister, Melissa, wants her to try and recover memories she’s lost. There’s a new person interfering; seemingly helpful, but he admits he is looking after his own interests.
A slight cliff-hanger leading into “Paper Clip”.