“Anasazi” is episode twenty-five of season two of The X-Files and the season finale.
The episode opens at the Navajo Reservation, Two Grey Hills, New Mexico, which is hit by an earthquake early in the morning. Later, a young man tells two older ones he is going riding. The older of the two mentions that the Earth has a secret it needs to tell. The young man sets off on a motorbike into the hills and finds that the path has been blocked by a rockfall. He climbs over it and notices in the quarry below something partially covered. Or, perhaps, partially uncovered. The something is metal and he returns home, telling the two men that he found something. Outside, kids are standing around whatever it is. The old man says, in Navajo, it should be returned. They will be coming. The thing looks to be the corpse of a Grey. The opening phrase is in Navajo, ‘Éí ‘Aaníígóó ‘Áhoot’é’, which means ‘The Truth is Out There.’
In Dove, Delaware, a computer is attempting to crack something whilst a man reads a book. It works, and the man is pleased with what he’s found and sticks a cassette into a drive to record it.
At the UN building in New York City, a man knocks on a door and tells another that someone has broken into the MJ documents. The recipient of the news rings another, and several more are rung, all of different nationalities. The last person phoned is the Smoking Man, who says it is already taken care of. Armed men break into the hacker’s place, but he’s gone.
Mulder is at home when there’s a knocking on the door. The three Lone Gunmen want to talk, even though Mulder says he isn’t feeling well. They say they weren’t followed by a multi-national black ops team who are looking for Kenneth Soona. They think that’s his real name; it’s the person they’ve referred to in the past as ‘The Thinker.’ Soona hacked the DoD computer system and got some data; his last communique asked for a meeting with Mulder in 3 hours. Although he may already be dead. At which point a gunshot rings out. One of Mulder’s neighbours has just shot and killed her husband of decades.
Mulder is at the meeting spot when Soona approaches. He claims he has the original DoD UFO intelligence files, from the 1940s up. Soona says he didn’t take any precautions, as he wasn’t expecting to get in. He wants the truth and for those responsible to answer to the people, handing Mulder an envelope.
At Mulder’s office, he opens the envelope to find the cassette. Scully arrives and says Skinner is looking for him. Mulder tells her he’s got the holy grail; evidence that the government has known about the existence of extra-terrestrials for 50 years. However, the files are not in English and Mulder gets, a bit irrationally, upset. The words look very similar to the Navajo of the title; Scully tells Mulder it may not be gibberish as she thinks it’s encrypted and that she recognises it. Her father told her about the Navajo Codetalkers of World War II.
Mulder does head to see Skinner, who says that there is a rumour Mulder has received sensitive files. Mulder is not being cooperative and ends up slugging Skinner, before being restrained. That, presumably like Mulder’s neighbour, was a bit out of character. The next day, Scully meets with Skinner and several others. They want to know if there’s a reason for Mulder’s bizarre behaviour. She says he’s been having trouble sleeping. There’s going to be a disciplinary hearing and, if they learn Scully has been keeping something from them, she will get the same summary action as Mulder. Dismissal with no chance of reinstatement.
Mulder’s father is at his home in Martha’s Vineyard when there’s a knock on the door. Through he frosted glass it looks like Mulder. Only it isn’t; it’s the Smoking Man. Who greets the elder Mulder by his first name; it seems the two know each other. He is there to tell Bill Mulder about the MJ files being taken. Files that Bill thinks should have been destroyed. Files that mention Bill Mulder by name. He is also concerned that no harm comes to his son; the Smoking Man says he doesn’t need a martyr.
Mulder is at home asleep and someone seems to be creeping up on him. It’s Scully; he wasn’t answering his door. Mulder isn’t feeling well. Nor looking well, for that matter. Scully wants to know if the files are worth it. He will let her know when he finds out what’s in them. Scully wants to know she is doing the right thing. So, Mulder tapes the window as his signal to Mr X – even though, in “Soft Light”, he said he didn’t want anything more to deal with him. Mulder has no explanation as to why he hit Skinner.
Scully is at the offices of the Navajo Nation in DC with a printout. The woman she is seeing recognises a word here or there, but to translate it will need an actual Codetalker. She knows a man. The words that jump out are ‘goods’ or ‘merchandise’ and ‘vaccination’ which are modern words.
Mulder is looking even worse when his father calls him and says he needs to see him. Scully arrives at Mulder’s apartment to find Mulder gone. And someone takes a shot at her. Mulder’s father tells him he’s going to hear things, words that will come to make sense. Related to ‘the merchandise.’
Krycek makes an appearance for the first time since he disappeared in “Ascension”. Mulder’s condition continues to deteriorate, and he gets very paranoid. The story continues in season three and “The Blessing Way”.