The X-Files: Season 3

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“The X-Files” is returning to FOX on January 24, 2016. Join Mieke Zamora-Mackay as she recaps each season for this popular TV show in preparation for the arrival of “The X-Files” Season 10.  In this post she recaps fan favorite and critically acclaimed season three.


This season is all about the connections and entanglements involving our lead characters. We learn that Fox’s family plays a much deeper role in the alien conspiracy that he is trying to unravel. The sacrifices that Fox and Dana are forced to make this season go beyond what you might think is humanly possible. We also get a chance to delve deeper into the character of their boss, Walter Skinner, making him an integral part of the X-files team, although he never does receive that lead character billing. We also see more of the Syndicate and their involvement in the world, as well as the introduction of an alien virus, that continues throughout the series canon. A recurring minor character who has brought me thorough enjoyment, Agent Pendrell, makes his debut.

Season 2’s finale “Anasazi”, and this season’s first two episodes forms a trilogy of episodes full of action and excitement, that sets the tone of rest of the season.

In “The Blessing Way” (S3: E1), we find that despite the bombing of the buried train car, Mulder managed to survive, but barely. It is a presumption that he managed to hide underneath the corpses he found to avoid detection. As he undergoes a healing “Blessing Way” ceremony led by the Navajo code breaker, Mulder has visions of his father and Deep Throat encouraging him to continue his quest to find the truth. Upon his recovery, he heads to his mother for answers about a photograph that shows his father with several other men, including the Cigarette Smoking Man (“CSM”) and Deep Throat. Teena Mulder can’t (or won’t) help him find the answers he seeks.

Meanwhile, Scully is thrown into whirlwind of doubt about who to trust within their circle, as Skinner seems more suspicious then ever. Especially after finds a small implant in her neck that turns out to be a sort of identification tag and data collection device. And when she is approached by the Well-Manicured Man at Bill Mulder’s funeral with a warning about the danger she is in, she is more than expecting that the person she must fear the most is her own boss.

WMM and Scully

As she confronts Skinner, her sister Melissa is mistaken for her and shot by the real bad guys, Alex Krycek and Luis Cardinal. Mulder finds Skinner and Scully in his apartment and breaks up the face-off in the beginning of “Paper Clip” (S3:2). Skinner claims to have the digital tape and he took it for safekeeping.

With the help of the Lone Gunmen, another person in the photograph is identified. Dr. Victor Klemper, a known Nazi scientist was brought to the US as part of Operation: Paperclip. The secret program that brought scientists and engineers from the Axis countries to avoid having their knowledge fall into the hands of the Soviet Union. Mulder posits that Dr. Klemper might have been working on the development of an alien-human hybrid. Melvin Frohike has the unfortunate task of informing Scully of the fate of Melissa.

Mulder discourages Scully from visiting Melissa, as she will surely be a target there. Instead, they pay a visit to Dr. Klemper, who identifies the location of the building in the photograph as a mining facility in West Virginia. Mulder and Scully head to the abandoned facility that houses another labyrinth of filing cabinets filled with medical records, namely of persons who received the smallpox vaccine. There they find a file for Samantha Mulder, as well as one for Dana. It appears that the file for Samantha was previously meant for Fox. While in the facility, Dana encounters several little creatures running though the labyrinth, while Fox encounters a UFO as they run from the Men In Black.

strughold mine

Upon their escape, Skinner informs the agents that he wishes to use the digital tape as leverage for their safety. Mulder agrees, but before Skinner is able to set up a meeting, the digital tape is taken from him in an attack by Krycek and Cardinal at the hospital where Samantha is being cared for.

The Syndicate has grown worrisome and distrustful of CSM, given his perceived failures of takin care of the Mulder and Scully problem. They want them killed, CSM insists they are more valuable to the “project” alive.

When Mulder and Scully return to the Dr. Klemper’s house for more information, they find the Well-Manicured Man. He admits that he knew Bill Mulder, and that they were part of a team that was gathered genetic data for identification purposes in the event of an apocalypse. He admits that Samantha was in fact taken to ensure Bill Mulder’s cooperation and silence about the experiments Klemper was performing.

Mulder returns this his mother and confronts her with the information he has just learned. She admits that it was Bill that chose Samantha to be taken instead of him. He then meets Scully at the hospital where he is informed that Melissa had passed away. In the meantime, Skinner negotiates with CSM, Fox and Dana’s safe return to the FBI.

In “Nisei” (S3:E9), Mulder purchases a video of what is claimed to be an alien autopsy. Convinced of its authenticity, he and Mulder pay a visit to the distributor in Allentown, Pennsylvania. When they arrive, they find the distributor murdered, and manage to chase down someone fleeing the scene. The individual turns out to be a high-ranking Japanese diplomat.

The agents are forced to release the diplomat, but not before they find a list of Mutual UFO Network (MUFON) members and Japanese satellite images of a ship at sea. The Lone Gunmen identify the ship as the Talapus, which just docked in West Virginia. Following the MUFON trail, Scully meets several women who claim to have been abducted, each having a microchip implanted in them, and each one dying cancer.

Mulder follows the ship trail and is led to a train yard where he observes what looks like an alien being transferred into a railcar in a train yard. The railcar is hooked on to a train and moves away. Mulder meets the train at some point and jumps on board from a bridge.

As Mulder makes his way on the train in “731” (S3:E10), Scully, with information provided by Agent Pendrell, heads to a former leper colony where her microchip implant was made. At the facility she learns that it had been a site where a Japanese scientist, brought to the United States like Dr. Klemper, had been testing on the patients. The effect of which made the patients look like aliens. This theory is confirmed by the First Elder of the Syndicate to Scully.

apolgy is policy

While in the railcar, Mulder finds a laboratory space and a quarantine room, inside of which is what he believes to be the alien. He also finds a journal of sorts, written in Japanese calligraphy. He is confronted by an assassin, who tells him that the being inside the room is a patient who has an immunity to biological warfare, which the Japanese scientist was trying to smuggle out of the country. The assassin, the Red-Haired Man, informs him that the US government would rather see the patient destroyed before having their research transferred into Japanese hands.

Scully reaches Mulder by phone and informs him that the alien in the car is in fact a human, who is infected with a form of hemorrhagic fever. She further informs him that there is a bomb on the railcar. With minutes to spare, X comes to the rescue and kills the Red-Haired Man. Not having enough time to save Mulder and the patient, he carries Mulder out to safety.

One of the major themes in the series mytharc is the black oil, also known as Purity, an alien virus that lived in petroleum deposits in the depths of the Pacific Ocean, is introduced in “Piper Maru” (S3:E15). The virus’ ship had been recovered by the salvage ship, the Piper Maru. This black oil has the ability to transfer and infect a person, and control that person’s behavior. It also has the ability protect itself and its host by creating a great pulse of energy that causes radiation burns to those that attack it. The black oil eventually makes its way back to United States when it infects Alex Krycek who was apparently selling the contents of the digital tape he stole from Skinner in Hong Kong. He claims it was his payback for how he was treated by CSM.


Back in the United States, Mulder and Krycek in “Apocrypha” (S3: E14), are run off the road by unidentified persons. While Mulder is knocked unconscious, the alien in Krycek protects him (or itself) and burns the men that attempted to capture him. Krycek manages to get back to CSM and returns the digital tape, in exchange for information on the location of where the salvaged space craft found by the Piper Maru was transferred.

With information on Krycek’s whereabouts, Mulder and Scully follow him to a series of decommissioned missile silos in North Dakota. Before the can get to him however, the agents are captured by the Men In Black and led away. In the meantime, Krycek has found the alien ship, and the black oil moves out of his body and seeps into its ship. The episode closes with Krycek banging on the steel door of the silo, begging to be let out.

In “Talitha Cumi” (S3:E24), we meet Jeremiah Smith, a seeming miracle man who can heal a person by laying his palms on them. In an odd twist, CSM pays Teena Mulder a visit at the family summer house. They are photographed in the midst of an argument. Sometime after that meeting, Teena suffers a stroke.

As Fox visits Teena in the hospital, she manages to scribble him a message on a note pad. This leads Fox to return to his childhood summer house and there her finds a stiletto weapon hidden inside one of the lamps. Believing that Jeremiah Smith can help him save is mother, he attempts to take him to see his mother, but the Alien Bounty Hunter arrives and gives chase.

This season saw a handful of now better-known actors and actresses playing various roles in the Monster of the Week episodes: Jack Black and Giovanni Ribisi in “D.P.O” (S3:E3), BD Wong and a very young Lucy Liu in “Hell Money” (S3: E19), and a teenaged Ryan Reynolds in “Syzygy” (S3, E 13). One of the episodes the brought both a tear to my eye and a hearty laugh was “Clyde Bruckman’s Final Repose” (S3L E4). Of course, no discussion of Season 3 would be complete without the mention of the self-poking episode, “Jose Chung’s From Outer Space” (S3: E20).

This season brought out the frustration in me that Mulder and Scully may never find the truth. I did however enjoy meeting Agent Pendrell, the forensic research agent that has such an obvious crush on Scully.


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