Part 1 of The X-Files Breakdown Seasons 1 – 3

January 9, 2016

Written by Capt McNeely

Georgia Division ZADF Twitter: @ZADF_ORG


The X-Files centers around two F.B.I. agents, Fox Mulder, the believer, and Dana Scully, the skeptic. The two spent 9 seasons and 2 major motion pictures investigating the strange and unexplained, all while hidden forces worked to impede their efforts. The X-Files was inspired by shows which featured elements of suspense and speculative fiction.

The two could not be more different, Mulder, a firm believer in the paranormal searches for the truth hidden in the government all while continuing his search for his abducted sister, Samantha. Scully, spent years studying to be an MD before changing careers and joining the F.B.I. Scully looks at everything from a scientific standpoint and is originally sent to debunk Agents Mulders work. While she agrees with Mulder through much of the series that certain things can not be explained, her and Mulder’s reasonings always differ.

The show offered multiple “monster-of-the-week” type episodes which were loosely based off “Alfred Hitchcock Presents,” “The Twilight Zone,” and “Tales from the Darkside.” The show took certain events from history and gave each event referenced a “spooky/what if” possibility. It also played along with and fed into the multiple 1990’s conspiracy theories which were popular during its run.


The very first episode is extremely important because it sets the tone throughout the rest of the series… while most fans would say Mulder and Scully started off with a friendship and eventually became romantically linked at the end of the series, I put out the theory that Mulder and Scully have been together (romantically) on and off again from the very first episode.

Over the next three weeks I will post an entire series recap that leans heavily on this theory. Each important episode and every monumental moment will be shared throughout 9 seasons, two features, and one run of comics (the official season 10) all leading up to the series revival on January 24th 2016!



Season 1 Episode 1 – “Pilot”

In the very first episode, we learn that talented F.B.I. agent Mulder, has been sent to the basement to work on The X-Files. Scully is sent to work with Mulder and ultimately disprove his work.

From the very first episode, we learn Scully has a fascination with Mulder and she admires his work ethic. While Mulder is unsure of her and what she will do to his “life’s work,” one thing is very clear, Scully deeply admires Mulder.

Halfway through the episode, while investigating an abduction case, Scully fears that the marks that have suddenly appeared on her back are the same ones that the kids who have been disappearing have. She enters Mulder’s hotel room, strips, and asks him to examine the marks on her back. While the marks turn out to just be mosquito bites, she hugs Mulder for an extended period of time.


This scene has never sat well with me. WHY would a woman (a medical doctor remind you) ask the opinion of “Spooky Mulder?” While the viewer does not know it at the time, it is a well known fact around the bureau that Mulder has a way with woman and is a “porn addict.” Scully would have known this the moment she entered his hotel room and took off her cloths.

Season 1 Episode 4 – “The Jersey Devil”

In episode 4, “The Jersey Devil” is a classic for fans because it is the first of many “monster-of-the-week” files and it is the first time we learn a little bit about Mulder and Scully. We learn Mulder has a porn addiction and Scully decides that she wants a life outside of work. Scully ends up going on a date with a boring man and then swears off dating. She realizes that what she wants is actually back at the office.

Season 1 Episode 8 – “Ice”

“Ice” is an unusual episode and the first in season 1 that I can say is an absolute favorite of mine. The agents head to Alaska to investigate a mass murder-suicide that occurs amongst a team of geophysicists. The two agents start to turn on each other as Scully believes Mulder is infected. It is only when they are alone that Mulder asks Scully to trust him.

While this is a little less than halfway through the first season, this “trust” based on blind faith becomes something that the two agents rely on.

Throughout the next few episodes things are good between Mulder and Scully. While David Duchovny and Gillian Anderson are creating witty banter to keep the viewers interested, their characters, Mulder and Scully, are building romantic relationship between each other, until…

Season 1 Episode 11 – “Fire”

In episode 11, “Fire,” where we learn a little about Mulder’s and his ex, Phoebe Green. Mulder and Phoebe spend some romantic time together and Scully is extremely jealous. She scolds her partner for most of the rest of the season for it. It was clear in “Fire,” that Scully thought they had something beyond a working relationship, Mulder did not.

Season 1 Episode 20 – “Tooms”

“Tooms” is an amazing episode (and fun fact, Eugene Tooms is the only “monster” villain who appears more than once). There is a lot going on in this episode, but one of the most important moments in X-Files history is when Scully tries to get close to Mulder and calls him by his first name, Fox. Mulder is taken back by this and immediately corrects her stating, “I even made my patents call me Mulder.”


Season 1 ends on a high, that really starts the whole X-Files alien human hybrid mythology. We learn the true intentions of The Cigarette Smoking Man (CSM), Mulder looses a friend/informant,  the truth about aliens on our planet, and find out that the X-Files has been shut down. Agents Mulder and Scully start to realize that they have become pawns in a much larger conflict and the two can only trust each other.


Season 2 Episode 1 – “Little Green Men”

Fun fact: This is the very first time we see an extraterrestrial on the X-Files.


Season 2 is filled with a large amount of information and it all starts with Scully taking extreme measures to get her ex-partner to notice her. When the two finally meet, she learns that Mulder has started to doubt the paranormal since his informant was murdered near the end of the first season.

With the X-files shut down, Mulder is thinking of leaving the F.B.I. However this fan-favorite monster episode entitled “Host,” just might be enough to keep him after a large flukewarm is found living in the sewers.

Mulder and Scully seem to be in a good place, until they meet Duane Barry.

Season 2 Episode 5 – “Duane Barry”


Duane Barry is an alleged alien abductee who has become violent. He refuses to take his medication and insists that Aliens are coming back for him. Barry eventually escapes and Mulder is sent to look for him with the help of fellow agent Alex Krycek.

Scully, always looking at things from a scientists point of view, decides to have a look at Barry’s medical files and soon releases that his frontal cortex was damaged when he was shot in the head in 1982. She assumes that he is lying about his abductions and warns Mulder.

Mulder does not write Barry off so quickly, as strange metallic objects where removed from Barry after he was placed in a hospital (remember this as it will become important in later seasons).

Barry escapes and kidnapps Scully. We do not know what really happened to Scully at this point, only that she is missing.

Mulder does everything he can to try to find her, but learns that Agent Krycek has a connection to The Smoking Man and a desperate Mulder tries to visit a Senator for answers, only to be discouraged by his new informant. Mulder soon realizes Krycek’s role in Scully’s abduction, and submits a report to his boss, Assistant Director Skinner. Skinner summons Krycek to his office, only to learn that he has disappeared. Skinner then announces the immediate re-opening the X-Files.

Season 2 Episode 8 – “One Breath”

Scully reappears in a coma at a hospital. She has multiple visions, but the most important one is one she shares with her father. Mulder, with the help of his geeky friends, The Lone Gunmen, learns that Scully’s DNA now contains hazadorous identification material which is killing her. Wanting answers, and being in a deep depression, Mulder storms into The Smoking Mans home and holds him at gunpoint. He demands answers and to know why Scully was ultimately abducted and not him.


The episode ends with Scully coming back to life.

Over the next few episodes, it has become apparent that Mulder is protecting Scully. While Scully trusts Mulder with her life, she refuses to tell him this because she fears he will treat her differently.

Season 2 Episode 13 – “Irresistible”

Mulder invites Scully to a basketball game, but unfortunately the agents have to cancel when they investigate the murders of Donnie Pfaster. From the start, Pfaster’s violent crimes did not sit well with Scully, she starts to doubt herself and her skills as an FBI agent. Scully becomes a victim of Pfaster’s and Mulder ends up saving her. She breaks down and cries taking comfort in Mulder. He tells her he has never thought of anything less than his equal, and that he can be trusted to help carry her emotional burdens as well as to watch her back.

Season 2 Episode 19 – “Dod Kalm”

“Dod Kalm” is actually one of my favorite episodes in the second season. In this episode, the agents investigate an abandon ship that is stuck at sea. While on board, the agents become trapped and soon realize that they are beginning to age rapidly. Within hours Mulder is an old man, barely holding on to life. Scully rushes to find a cure for not only her partner, but herself as well.

There are a lot of beautiful moments between Mulder and Scully in this episode, from snuggling up together to neither of them wanting to drink the purified water because each one can’t live without the other. For anyone who believes the theory that Mulder and Scully have been together from the beginning, I would suggest giving this episode another watch and carefully listen and “decode” what the agents are really saying to each other.


Just like season 1, season 2 ends on a high. We learn of Alien bounty hunters, unravel more of the X-Files mythology between Alien Human Hybrids and the survival of our planet, and discover what really happened to Mulder’s sister (up until this point). Mulder and the Smoking Man race against time to hear classified information on a digital tape.


Season 3 begins on a high. In the second episode, “Paperclip,” Scully is set to be murdered. A gunman waits in Scully’s apartment and as soon as her front door opens, the gunman fires, causing a bloody mess and a body to fall to the ground, only it wasn’t Scully, it was her sister Melissa.


Over the next few episodes throughout season 3, it becomes apparent that Mulder and Scully’s relationship has began to suffer due to the lose of Melissa. Scully has realized that while chasing spooks with Mulder was somewhat abnormal, it has now become dangerous and has become HER life’s work to bring the men who killed her sister to justice.

She never comes out to say that she blames Mulder for her sister’s death, but Mulder starts to blame himself. Mulder becomes very angry and distances himself from Scully.

We see Mulder start to flirt with other woman, such as Bambi Berenbaum in “War of the Coprophages,” and Scully is clearly jealous. Throughout most of season 3, Scully is short with Mulder and angry at him for giving up on their relationship.

Season 3 Episode 13 – “Syzygy”

This entire episode is hard to watch, because from the beginning I have rooted for Mulder and Scully, but this episode clearly shows that the two agents are in very different/angry places. Mulder shows interest in a female detective while Scully becomes insecure about herself. The episode ends with the two agents arguing in a car and Scully telling Mulder to “Shut up!”

Season 3 Episode 17 – “Pusher”

The agents spend some time investigating a psychokenetic killer by the name of Robert Modell. The episode ends with a game of Russian Roulette and Scully grabbing Mulders hand with a reassuring squeeze and tells him she’s not going to let Modell take up any more of their time. It is one of the first times we see the agents touch when no physical contact was needed.

For the next few episodes, the agents once again begin to get closer as playful banter can be seen throughout the Season 3.

Season 3 Episode 22 – “Quagmire”

While the agents investigate a modern day Loc Ness Monster, the two become stranded on a rock after their boat sinks.

While one could look at this episode and think it has nothing to do with the overall X-Files mythology, I will say that it in fact DOES, as it plays an important role in Mulder and Scully’s relationship.


Needing to stay warm, the two get a little close and Scully opens up for the first time all season, we learn about her childhood and how she shared moments growing up with her father (think back to season 2’s “One Breath).”

Scully shares a very important Moby Dick story with Mulder and ultimately makes a reference about how Mulder is constantly searching for his “white whale…” but what Scully doesn’t realize is she is constantly searching for hers in Mulder.


Season 3 Episode 23 – “Wetwired”

While there was one more episode in season 3, I believe THIS should have been the last episode of the season. While on a case, Scully decides to watch some videotapes to see if they can catch a man who committed a murder. While taking a break Scully heads outside to see Mulder talking in a car to The Cigarette Smoking Man. Scully is shocked to see Mulder with their enemy. The next morning Scully asks Mulder about the conversation and Mulder lies, stating he never saw the Smoking Man.

Which leads into an unforgettable ending to season 3, which will be covered next week!


Feel free to let me know what you thought via the comment section or via Facebook messenger! Do you agree or disagree?

Attached below is some info on the new season as well!

The X-Files Re-Opened Documentary

The X-Files First Look Season 10 

The X-Files Comes to Blu-Ray

Gillian Anderson’s “Show & Tell”

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