The episode was directed by R. W. Goodwin, and featured guest appearances by Peter Donat, Nicholas Lea, Mitch Pileggi and Floyd Red Crow Westerman.

The show centers on FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) who work on cases linked to the paranormal, called X-Files.

He retrieves the corpse of an alien-like figure from the boxcar, which he takes back to the reservation and presents to the residents, including a Navajo elder named Albert Hosteen.

Shortly afterward, Kenneth Soona, a computer hacker known as "The Thinker", breaks into the Defense Department database and downloads secret files related to extraterrestrial life, putting them onto a digital tape.

When the Syndicate, a secretive group of government officials, learns of the breach, the Smoking Man tells them that he has already resolved the matter, although this is a lie.

Scully brings an unconscious Mulder to New Mexico and, when he awakens, reveals that his behavior was caused by a drug placed into his water supply and that she shot him because if he had killed Krycek, it would have been harder to prove his innocence in his father's death.

Generally, when we pitch stories to the staff everyone comments on them, and Darin Morgan called this the kitchen sink episode, because it had so much in it, he didn't know how we would pull it off.

[3] The episode tried to make similar cliffhangers as the previous season finale, with revelations such as Mulder's father being part of the conspiracy and later killed to "prove anything could happen in The X-Files".

[6] When early seasons of the show were re-released in 16:9 widescreen for home video and streaming services in 2016, this practical effect became noticeable as sections of gray, unpainted quarry were visible at the edges of the frame which would not have been viewable on 4:3 televisions at the time of the original broadcast.

[7] To create the impression of a buried train carriage, a depression had to be blown into the ground and thirty-two dump trucks worth of debris removed.

[14] In a retrospective of the second season in Entertainment Weekly, "Anasazi" was rated an A, being described as "mind-blowing if frustrating", with it being noted that the episode "made fans want to fast-forward through summer.

However, he felt that the episode marked the point at which the series' overarching mythology would begin to lose focus, explaining that "it's troubling that instead of answering any big issues here ... the show only gives us new directions".

While writing a largely positive review of the episode, Jess Camacho of Multiversity Comics argued that "Anasazi" is "awful when it comes to dealing with Native American people, specifically their very valid conflicts with the U.S. government.

"[18] Likewise, Eleanor Hersey, in an article published in the Journal of Popular Film & Television argues that "The X-Files is certainly guilty of romanticizing and stereotyping the Navajo" in the episode.

[19] Conversely, Caroline M. Woidat, in her journal article "The Truth Is on the Reservation: American Indians and Conspiracy Culture", argues that "a shared passion for revealing the government’s lies and secrets forges a common bond between Mulder and Hosteen [and this] pairing allows for pointed social critique: 'One of the most compelling aspects of the "Anasazi" arc is its representation of X-Files mythology and Navajo mythology as alternatives to the national narrative in which all traces of government misconduct and cultural genocide are always erased'.