X-Files Season 7-9 Breakdown Part 3

January 23, 2016


Written by Capt McNeely

Georgia Division ZADF Twitter: @ZADF_ORG

First, thank you to those fellow fans who have taken the time to read my recap and listen to some of my theories.

We are ONE day away from the start of the X-Files Revival on FOX which means it is time to cover season 7 – 9 and well as the last film, “I Want To Believe.”


If you need a refresher here are parts 1 and 2:

PART 1 Season 1-3

PART 2 Season 4-6


Season 6 ends with “Biogenesis,” which brings new aspects to the series overarching mythology.

The episode begins with a biology professor, Merkmallen, in West Africa placing two metallic objects together. When the two objects meet they hover in the air and fly across the room landing in a bible. This man takes the objects to a professor in the United States named Sandoz, who has a similar piece. An alien bounty hunter disguises himself as Sandoz and kills Merkmallen.  The real Sandoz discovers the murdered corpse and flees.

Assistant Director Skinner assigns Mulder and Scully to investigate the disappearance. Mulder believes the men had where trying to bring an extraterrestrial origin to life on Earth.

Mulder soon falls ill and the agents learn that the artifact is originally Navajo. Scully heads to the southwest to learn that the artifact has passages from the bible.

Season 7 Episode 1 & 2 – “The Sixth Extinction”

Mulder’s condition worsens and Agent Fowley offers to take care of him. Mulder is led to believe the artifact proves that humanity was in fact created by aliens.

Fowley soon contacts the Cigarette Smoking Man and Mulder’s condition soon spirals out of control. Mulder ends up in a padded cell and starts displaying abnormal brain activity.

Scully heads to West Africa to find a cure for Mulder and learns the artifacts are part of a much larger spacecraft which was buried in the sand.

Skinner starts doing his own investigation and is led to a man by the name of Kritschgau who believed Mulder has an alien induced min and injects him with a drug to slow down his brain activity. Later that evening Mulder tells Skinner that he knows about his alliances to Alex Krycek. He also tells Agent Fowley that he knows of her connections to the Cigarette Smoking Man.

Scully continues to search for answers and starts decoding the spacecraft which contains information on genetics and various religions. Scully leaves to check on Mulder at the hospital who is now completely paralyzed.

The Cigarette Smoking Man and Mulder’s mother enter Mulder’s hospital room and we learn that The Smoking Man is actually Mulder’s father. The Cigarette Smoking Man removes him from the hospital and takes him to a secret government location (Mulder goes missing).

Skinner’s informant Kritschgau tells Scully that Mulder was infected with the “black oil” three years early and because he is infected, Mulder is proof of alien life.

The Cigarette Smoking Man takes Mulder to meet his sister Samantha, and buys him a home in a well off neighborhood. Mulder decides to spend the rest of his life with Diana Fowley, his only love. Everything seems to good to be true, and it is… Mulder is dreaming.

Mulder is actually in the middle of brain surgery while The Cigarette Smoking Man and Agent Fowley watch. The Cigarette Smoking Man is preparing to have part of Mulder’s brain removed and implanted into himself. The Cigarette Smoking Man believes that Mulder has become an alien human hybrid and by taking his genetic material he will survive the alien apocalypse.

In Mulder’s dream, we see him accompanied by The Cigarette Smoking Man who informs him that everyone he knows has died and now it is Mulder’s time to go. Mulder is relieved and ready to die, but he wonders where Scully is. Mulder will not “let go” until he has answers, even in what The Cigarette Smoking Man thought was Mulder’s “ideal” world.

Meanwhile, Fowley slips a security card under Scully’s door that eventually leads her to Mulder. Scully convinces Mulder to leave his dream and come back to her… reality.

A short time after Fowley is killed for helping Scully and she is unsure how to tell Mulder the news. Mulder is upset, but reveals to Scully that SHE is his “touchtone.”

Season 7 Episode 4 – “Millenium”

“Millennium” is important for two reasons, we learn that a group of men believe in the year 2000 the alien apacolypse will start with the new year, and this is also the FIRST time we see the agents share a romantic kiss as Mulder leans in to kiss Scully on New Years Eve.

The next few episodes are a testament to the fact that Mulder and Scully are in a good place together despite the fact that Donnie Pfaster makes a reappearance and once again goes after Scully.

Season 7 Episode 15 – “En Ami”

Things with Mulder and Scully are good until Mulder catches Sculyl with The Cigarette Smoking Man. The Cigarette Smoking Man tells Scully that he wants to atone for all his bad behavior and that he is dying from his operation preformed at the beginning of the season. Scully kitty’s him and agrees to help as he is being nice to her. Mulder can’t believe how stupid she is acting and tells her he can’t even look at her.

Scully ends up being used as a pawn in The Cigarette Smoking Man’s game and while she thinks she received a disk, she soon learns that The Cigarette Smoking Man deceived her and swapped out the real disc.

Season 7 Episode 17 – “All Things”

“All things” begins with Scully getting dressed in Mulder’s bathroom as Mulder lay sleeping in his bed. She states:

“Time passes in moments… moments which, rushing past, define the path of a life, just as surely as they lead towards its end. How rarely do we stop to examine that path, to see the reasons why all things happen, to consider whether the path we take in life is our own making, or simply one into which we drift with eyes closed. But what if we could stop, pause to take stock of each precious moment before it passes? Might we then see the endless forks in the road that have shaped a life? And, seeing those choices, choose another path?”

The viewer is led to believe that the two have slept together, although this is a rewind episode and the events that happened previously are described below.

The entire episode revolves around Scully having a former flame come into her life. The man is extremely sick and is in the hospital begging Scully to take him back as he still loves her.

This episode is EXTREMELY important in Scully’s storyline and in cementing the fact that the two are actually together as a couple. Scully reveals that she left this man and officially took her career at the F.B.I. after being assigned to the X-Files. While this man WAS at ONE TIME, the love of her life (and she will admit that), she has now realized her path lays elsewhere (with Mulder). While at one time she wanted a family and to be a mother, she has now moved on and is on the same path as Mulder, and she accepts that for the first time in the entire series.

Scully goes to Mulder’s apartment and falls asleep on his shoulder, finally realizing that THIS is where she belongs.

Season 7 Episode 19 – “Hollywood A.D.”

“Hollywood A.D.” is important a fan favorite and it is important in proving that Mulder and Scully are together because while the shows episode is in Season 7, the events that happened in the episode actually took places a few seasons before.

The episode opens with Mulder and Scully sitting in a movie theatre watching a blockbuster movie made about their career as agents in the F.B.I. Mulder shakes his head at just how bad the movie is and exits the theatre.

We are shown a flashback in which we see a writer accompany them on a case. The film tells the story of how the WRITER sees Mulder and Scully’s relationship.

Flashback to present day, Scully exits the theatre to look for Mulder. She finds him sitting alone on a deserted soundstage and he states, “They got it so wrong Scully.” Meaning: Scully was the one to fall in love with Mulder, not the other way around. Mulder looks like a fool on screen, when in actuality (and throughout the series) Scully was the one who looked foolish/jealous at times.

The episode ends with Scully holding Mulder’s hand as the two exit a soundstage.

Season 7 Episode 20 – “Fight Club”

Mulder shows Scully a case in which two agents resembling themselves at the Kansas Field Office have brutally beaten each other up. Mulder states that the two agents have been together for 7 years. Scully questions him and is surprised as her and Mulder have been together exactly 7 years… Mulder quickly corrects her, “but they are NOT romantically involved.”

Does this mean that our two agents, Mulder and Scully are? YES!

Season 7 Episode 22 – “Requiem”

“Requiem” goes all the way back to the beginning as the agents are called back to their very first case in Oregon dealing with alien abductions and missing teens.

Mulder believes and is led to believe by Krycek that a UFO is hidden in the forest within in energy field.

Scully seems off and unwell. Mulder soon realizes he has once again put her life in danger as she is an alien abductee and the spacecraft is taking previous abductees. The two spend and evening cuddling together and he kissed her and tells her he will not let anything happen to her.

Krycek informs Mulder that the UFO is hidden in an energy field.

Regardless of her ill feelings, Scully heads out into the field and is frozen in time and pushed back/away from the spacecraft. She soon realizes that the spacecraft doesn’t want her… but there is someone it DOES want.

Mulder wanders out into the field and is abducted onto a spacecraft.

He is officially missing and Scully ends up in the hospital.

Season 7 ends with Scully telling Skinner she MUST find him because she is pregnant.

As much as I love the X-Files, the next few seasons were a bit hard for me to rewatch. For those who are unaware, the actors David Duchovny and Gillian Anderson were not getting along in real life. Duchovny thought it was time for him to leave the series and become a “movie star.”

FOX executives searched for a replacement while Duchovny finished out his contract, that replacement was found in Terminator 2, action star Robert Patrick (if you’re a horror fan you might remember him from the cult classic “The Faculty).”

FOX decided Anderson and Patrick would be a good fit and could keep the show going… so…

Season 8 begins with Scully and Skinner frantically searching for answers as to what happened to Mulder.

The F.B.I. has reason to believe Mulder has deserted them and planned his own death.

Agent John Doggett (Robert Patrick) is assigned to search for Mulder.

Scully instantly does not trust Doggett as he tells her that Mulder was a bit of a womanizer. Scully tells him that he doesn’t know Mulder at all.

Doggett soon discovers that Mulder was dying of a rare desease and had known about it for months. Scully can’t seem to believe this despite the fact that all the evidence points to it being entirely possible.

Doggett, being a skeptic, refuses to believe in anything Skinner or Scully tell him.

The Agents all eventually end up searching for Gibson Praise as they believe the young boy has become a target for alien human hybrids, Alien Bounty Hunters, and “Super Soldiers (which is mentioned but we will cover more later on).”

Doggett is officially assigned to the X-Files full time and Scully decided to keep her pregnancy from him for most of season 8.

Season 8 Episode 13 – “Per Manum”

Halfway though Season 8, Scully begins to question the origins of her pregnancy as multiple alien abductees have all been killed shortly after giving birth to alien babies.

We are shown flashbacks of Mulder telling Scully that her abduction has rendered her infertile.

Regardless of the bad news, we see Scully ask Mulder to be the father of her baby. Mulder says yes however he worries that this child will come between them (remember this line, as this will be a MAJOR plot point in the newest season).

Scully goes to the doctor in a later flashback thinking she is pregnant and finds out that she is in fact, NOT. Mulder awaits at her apartment to hopefully hear good news, but is devastated by the results. He comforts Scully and tells her, “never give up on miracle.”

Back in real time, Doggett soon realizes that Scully is pregnant when she checks herself into a secret military base for further testing.

Scully is lied to multiple times throughout the episode as “Super Soldiers” all tell her her baby is normal.

This episode is important because it wants you to believe that Scully’s baby is alien, but it is actually Mulder’s child.

Doggett asks Scully why she didn’t tell him she was pregnant and she explains that she feared if she told him she would be taken off the X-Files. Scully begins to cry and Dogget tells her THEY WILL FIND HIM (Mulder) and that he is here to help.

It is at this moment that the two Agents really begin to trust each other and become partners.

Season 8 Episode 14 – “This is Not Happening”

This marks the return of Mulder as a UFO starts to return alien abductees.

An old friend, Jeremiah Smith, starts taking the bodies and “healing” them as the UFO is giving back dead bodies.

A new agent, Monica Reyes, is brought in to help find the body of the returned Fox Mulder.

It is then that we learn that Agent Doggett has worked with Agent Reyes in the past and he had a son that was found dead. Doggett starts to really feel for Scully when Mulder is found dead and Jeremiah Smith is nowhere to be found.

Season 8 Episode 15 – “DeadAlive”

Mulder is officially laid to rest, but Skinner decides to dig up the body late one night as other alien abductees have been coming back to life, specifically Billy Miles. Skinner does not realize though that the abductees are returning as “Super Soldiers,” the next stage in Alien Evolution, a human alien replica replacement.

Skinner and Scully put Mulder on life-support and hopes for the best.

Skinner is soon met by Krycek and Krycek reveals that there is a vaccine for Mulder to survive the alien virus. Krycek will give skinner the vaccine, but he requests thst scully does not come to full term with the baby as she is carrying a human hybrid.

Skinner realizes he CANT do that to Scully and pulls Mulder off life support hoping it will finally kill him. Skinner didn’t realize that pulling Mulder off life support will put the alien virus at bay.

Mulder goes through some transfusions and is seemingly healthy when he awakes.

Season 8 Episode 16 – “Three Words”

“Three Words” opens with a chase as man rushes the White House demanding that he needs to inform the president that aliens are taking over the United states. The man ends up shooting himself and hands a disk over to an officer that reads “FIGHT THE FUTURE.”

This is the start to what will lead to the end of the X-Files mythology in the first 9 seasons.

Things between Mulder and Scully are not good, as Mulder has no idea where he fits in (at this point he isn’t even sure if the baby is his). Scully tells Mulder she loves him and that she is thankful that all her prayers have been answered and she has him back, BUT something is off. He tells her he is having trouble processing everything (including the baby).

Doggett soon learns that he and Scully have a higher success rate in the X-Files in the few months they have been working together than Mulder and Scully had in over 7 years. The F.B.I. is trying to fire Mulder. Scully goes to tell Mulder the bad news and he says “your going to have a baby in a few months and wont have time for the X-Files.”

Mulder is starting to wonder if the baby will be what ends his life’s work… If Scully is not there, who will want to do the X-Files? He decides it is time to go back to work.

Doggett soon realizes that he is being used… No one trusts him and an old friend, military man Rohrer, threatens him (Doggett is unaware that this friend is in fact a “Super Soldier).”

The Agents soon learn that “FIGHT THE FUTURE,” is a password that unlocks government data and links DNA profiling and replacement for alien human hybrids.

Season 8 Episode 17 – “Empedocles”

Scully is hospitalized as her placenta has torn away from the uterine wall.

Mulder starts investigating a case with Agent Reyes but is thrown off track when Doggett wonders why Mulder is looking into his past.

This episode is important because it cements the fact that all four agents, Mulder, Scully, Doggett, and Reyes are a team who will protect each other at any cost while searching for the truth.

In the next few episodes Mulder is officially fire, but feels confident that Doggett will keep the X-Files alive and hopefully give them a bit of credibility now that he has left.

Scully goes on maternity leave and Doggett wonders if she will be back.

Season 8 Episode 20 – “Essence”

“Essence” opens with a powerful quote from Mulder.

“We call it the miracle of life: Conception. A union of perfect opposites. Essence transforming into existence, an act without which mankind would not exist and humanity cease to exist. Or is this just nostalgia now? An act of biology commandeered by modern science and technology. God-like we extract, implant, inseminate and we clone. But has our ingenuity rendered the miracle into a simple trick? In the artifice of replicating life can we become the creator? Then what of the soul? Can it too be replicated? Does it live in this matter we call DNA? Or is its placement the opposite of artifice, capable only by God? How did this child come to be? What set its heart beating? Is it the product of a union or the work of a divine hand? An answered prayer, a true miracle? Or is it a wonder of technology? The intervention of other hands? What do I tell this child about to be born? What do I tell Scully? What do I tell myself?”

This quote leaves you wondering many things… but ultimately, it leaves you wondering if the child was artificially inceminated or conceived naturally. Is Mulder the father?

Skinner starts poking around and tells Mulder he needs to know who the father of the baby is. Mulder plays is sly and acts as if he doesn’t know. Mulder ultimately tells Skinner that if he wants to know, to ask Scully.

Super Soldier Billy Miles appears and starts killing Drs who have preformed experiments on alien bodies. Doggett, Reyes, Mulder, and Skinner fear for Scully’s life as Miles is now searching for her.

Scully cries in Mulders arms and tells him she can’t live her life as an X-File. Mulder tells her this isn’t about the X-Files anymore, its only about her. He will protect her and her baby at all costs.

Billy Miles appears at Scully’s apartment and the two agents are on the run. They make a last minute decision and decide to trust Alex Krycek who ends up running over Miles with his car.

Krycek soon reveals that Scully’s baby is in fact a miracle, more human than human.

The aliens fear the fact that there is a higher power than them, GOD.

Season 8’s finally ends with Dogget’s military man Rohrer trying to cover Krycek’s tracks and tells him that Miles can not be stopped as he is a Super Solider. He informs Doggett that Scully was taken in a military experiment that was staged as an abduction and that the chip in her neck got her pregnant.

Doggett begins to question Rohrer and him and Mulder search for their own answers and Doggett asks Mulder when this is all going to end.

Skinner makes a quick decision and ends up killing Krycek as Krycek holds a gun to Mulder and Doggett ends up killing Rohrer.

Scully is transported to a secret location to give birth with the help of Agent Reyes.

Regardless of how well the agents hid their tracks, Super Soldier Miles ends up finding Scully and watches the birth of the child with a group of Alien Human Hybrids, they themselves wanted to witness the miracle.

Doggett assigns Agent Reyes to work with I’m on the X-Files and tells F.B.I. deputy director Kirsch that he is planing to investigate him for covering up evidence of Aliens in the Government.

The season ends with Mulder and Scully in Scully’s apartment… Scully doesn’t understand as she thought that the hybrids were there to take the baby and that from the moment she became pregnant she has feared the truth.

Mulder says the truth is something they both know. They kiss and the camera pulls back ending season 8.

Season 9 – Episode 1 & 2 “Nothing Important Happened Today”

Season 9 starts 48 hours after Scully gives birth.

Mulder is in the shower and Scully picks up a crying William. She heads out to here living room and places in front of her is pile of luggage.

Doggett heads to Mulder’s apartment to search for answers and look into the deputy director. When he arrives at Mulder’s apartment, he soon realizes that Mulder has disappeared.

Doggett immediately goes to Scully’s apartment and Scully tells him Mulder is officially gone.

Doggett and Reyes meet with Skinner who tells them to drop the case against Deputy Director Kirsch and pleads for Milder and Scullys life, but especially the life of young William. Doggett refuses to drop the case.

Doggett once again goes to Scully. He pushes her for answers, Scully asks him to leave and not come back.

She soon realizes she is wrong after she awakes to a supernatural power that she believes is coming from young William.

Agent Doggett and Reyes spend most of season investigating random X-Files and the incidences that lead up to William’s birth and Scully starts teaching at the F.B.I. Academy.

Season 9 Episode 6 – “Trust No 1”

“Trust No 1” opens with a quote from Scully that mimics a quote from Mulder earlier (see quote above from season 8):

“One day, you’ll ask me to speak of a truth – of the miracle of your birth. To explain what is unexplained. And if I falter or fail on this day, know there is an answer, my child, a sacred imperishable truth, but one you may never hope to find alone. Chance meeting your perfect other, your perfect opposite – your protector and endangerer. Chance embarking with this other on the greatest of journeys – a search for truths fugitive and imponderable. If one day this chance may befall you, my son, do not fail or falter to seize it. The truths are out there. And if one day you should behold a miracle, as I have in you, you will learn the truth is not found in science, or on some unseen plane, but by looking into your own heart. And in that moment you will be blessed – and stricken. For the truest truths, are what hold us together, or keep us painfully, desperately apart.”

Scully begins to wonder if something is wrong with her son.

A man appears to Scully and tells her he needs to talk to Mulder and can save their lives.

She does not realize that he is a Super Solider looking to kill Mulder.

Scully pulls Mulder out of hiding but fails at seeing him as the Super Solider acts to quickly and ends up showing a weakness, a rare metal that can kill any Super Solider.

A plan is soon set into motion by a cult to kill baby William.

Season 9 Episode 16 – “William”

This episode is painful… Agents Doggett, Reyes, and Skinner all believe a disfigured man that has broken into the X-Files is in fact Fox Mulder. Scully refuses to believe this despite the fact that a DNA test proves it to be an identical match to Mulder.

Scully hides the man in her apartment and one night the man inject baby William with a strange substance. The substance turns out to be something that cures young William of any alien DNA.

The man turns out to be ex Agent Jeffery Spender, he has the same DNA as Mulder for they have the same biological father, The Smoking Man.

Spender tells Scully that the baby might be cured of the alien virus, but ultimately that “they” will always be looking for young William and when they find him they will do the same test on William that they have done to him.

Scully makes a difficult choice and decides to place William up for adoption.

Season 9 Episode 19 “The Truth”

If you only have time to see ONE X-Files episode before tomorrow night, make it this one!

The series finale ends with Mulder learning that the Alien Invasion date and official takeover in on December 22nd, 2012.

Mulder is put on trial for killing Super Soldier Rohrer inside a secret government facility. Everyone from the X-Files is present in this series recap as Mulder and Skinner testify against a group of Military men who ultimately decide that Mulder must be silenced by lethal injection.

The X-Files is officially shut down and the office is destroyed.

Deputy Director Kirsch realizes he made a mistake and catches Skinner and Doggett breaking Mulder out of a military prison, instead of turning them in, he decides to help them.

Mulder and Scully head south to New Mexico to meet with an ancient man who claims to have information about the the invasion.

They arrive to the ancient ruins and discover The Cigarette Smoking Man hiding out in caves that are rich with the deposits of iron that can kill the Super Soldiers. He believes that hiding out here will save him from the inevitable invasion.

Mulder realizes The Cigarette Smoking Man is foolish and the agents leave just before the military blow up the caves.

The show ends beautifully with Mulder and Scully inside a hotel room in Roswell NM, (much like the series began with them in a hotel room). Mulder admits that he kept the 2012 date a secret from Scully because he didn’t want to believe it, hurt or worry her.

Scully tells him that when she started she instantly fell in love with him (which once again cements my theory that they have been together the whole time) and that his beliefs are what kept her going through everything (even William, which they admit is “their” son).

From a character standpoint, fans could not have asked for a better ending. We now see the two agents viewpoints are very different from where they started… The believer now has hope in humanity and in god and Scully believes in the impossible.


In 2008, fans were delighted to see Mulder and Scully back, in movie form that is.

In 2008’s “I Want To Believe,” we see Mulder and Scully in present day.

Mulder is still wanted by the F.B.I. and is hiding out at Scully’s.

Scully has left the F.B.I. and is now a full time medical doctor at a local Catholic hospital.

Scully is asked to bring Mulder into the F.B.I. to help with a paranormal case, Mulder agrees but only if Scully works with him.

The two agents spend time arguing about who they are and where they fit into society. Scully tells Mulder that his stubbornness is why she fell in love with him, but Mulder ultimately knows that on some level that is also why they can never be together.

The film revolves heavily around Scully and the heart wrenching decision she made in season 9 to give up young William.

Scully tells Mulder she can not live her life in the darkness anymore.

Could this be the reason the two agents are not together in the revival series?

We will have to wait and see! The X-Files premiers tomorrow night on FOX after the football game (roughly 9pm).

As always, feel free to let me know what you thought via the comment section or via Facebook messenger!

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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