The 17 best The X-Files episodes that feature Aliens and the Alien Conspiracy

17 March 2023
The X-Files was an iconic television show that captivated audiences with its masterful storytelling and gripping exploration of the unknown. At the heart of the show was its grand alien colonization theme, which added a level of depth and intrigue that elevated it above other shows of its time.

Through its portrayal of the vast, complex conspiracy of extraterrestrial life and its influence on Earth, The X-Files explored some of the most compelling themes of the 1990s. Its characters, particularly the dynamic duo of Mulder and Scully, were expertly crafted and brought to life by David Duchovny and Gillian Anderson, who imbued them with a sense of humanity and vulnerability that made them relatable to audiences.

But what really set The X-Files apart was its willingness to delve into the unknown and to explore the darker aspects of humanity's relationship with the unknown. Its portrayal of alien colonization was both haunting and awe-inspiring, tapping into our deepest fears and desires about what might be out there beyond our world. 

All while the Cancer Man hindered them at most turns... he was such a father figure eh?

Anasazi xfiles alien

The X-Files also tackled some of the most pressing issues of its time, such as government conspiracies, cover-ups, and the dangers of technology, all of which resonated deeply with audiences. 

All in all, The X-Files was a masterpiece of science fiction storytelling that left a profound impact on its viewers. Its grand alien colonization themes and stories, coupled with its masterful storytelling and unforgettable characters, made it one of the most compelling TV shows of the 1990s and a true cultural phenomenon that still endures to this day.

Here is a list of some of the best-reviewed and highest-rated episodes of The X-Files that features aliens or the alien conspiracy:

    xfiles alien colonist creature
    The truth is here...
  1. "Pilot" (Season 1, Episode 1)

    Mulder and Scully are assigned to investigate the mysterious deaths of several teenagers in Bellefleur, Oregon. Mulder believes these deaths are linked to alien abductions, while Scully remains skeptical. The case sets the tone for their partnership, balancing Mulder's belief in the paranormal with Scully's scientific skepticism. Ultimately, they find evidence suggesting alien involvement, but it is destroyed, leaving the truth elusive.

    This episode was shot in 12 days, using fake rain due to the lack of actual rain in Vancouver. The pilot was a test for the series, with Fox unsure of the show's potential success.

    "Duane Barry" (Season 2, Episode 5)

    Mulder and Scully investigate Duane Barry, a former FBI agent who claims to have been abducted by aliens multiple times. Barry takes hostages in a travel agency, demanding to be taken to a UFO hotspot. Mulder negotiates with Barry and discovers that Barry's abductions may be linked to an alien implant in his body. The episode ends on a cliffhanger, leading directly into the next episode, "Ascension."

    Directed by Chris Carter, this episode won an Emmy for Outstanding Individual Achievement in Sound Editing. It also marks the beginning of a major story arc involving Scully's abduction.

    "Anasazi" (Season 2, Episode 25)

    Mulder receives a digital tape containing secret government files, revealing a conspiracy involving the government and extraterrestrials. As he delves deeper, he becomes increasingly paranoid and violent, possibly due to a substance in his water supply. Meanwhile, Scully uncovers evidence that could exonerate Mulder's father, who is later murdered. The episode ends with Mulder trapped in a boxcar filled with alien corpses, which is set on fire by a mysterious assassin.

    This episode was originally intended to be the season finale, but the network ordered three additional episodes. The boxcar scene was filmed in the Mojave Desert, a rare departure from Vancouver.

    "Nisei" (Season 3, Episode 9)

    Mulder and Scully investigate a videotape showing an alleged alien autopsy. Their investigation leads them to a group of Japanese scientists conducting secret experiments on alien technology. Mulder boards a train carrying an alien-human hybrid, while Scully uncovers her own connection to these experiments. The episode ends with Mulder in mortal danger, trapped in a train car rigged to explode.

    The title "Nisei" refers to second-generation Japanese-Americans, a reference to the scientists involved. This episode is part of a larger arc exploring Scully's abduction and its aftermath.

    "Memento Mori" (Season 4, Episode 14)

    Scully discovers she has terminal cancer, likely linked to her earlier abduction. As she investigates other women with similar diagnoses, she uncovers disturbing evidence that her cancer is part of the larger alien conspiracy. Mulder becomes desperate to save her, pursuing leads that bring him into conflict with the shadowy figures behind the conspiracy. The episode is emotionally charged, focusing on Scully's vulnerability and Mulder's determination.

    Written by Gillian Anderson, this episode won an Emmy for Outstanding Writing for a Drama Series. The title "Memento Mori" is Latin for "Remember you must die," reflecting the episode's themes.

    "Patient X" (Season 5, Episode 13)

    Mulder and Scully are drawn into a new phase of the alien conspiracy when they investigate a series of mass burnings of abductees. They meet Cassandra Spender, who claims to be a multiple abductee and the key to understanding the alien agenda. Mulder, now skeptical of alien involvement, believes the events are a government hoax. The episode ends with a mass abduction witnessed by Scully, shaking her faith in her scientific beliefs.

    This episode marks the return of Chris Carter as director after a two-year hiatus. It also introduces the character of Cassandra Spender, who plays a significant role in the unfolding mythology.

    "The Red and the Black" (Season 5, Episode 14)

    Continuing from "Patient X," the episode follows Mulder and Scully as they investigate the aftermath of the mass abduction. Mulder begins to believe that the alien colonists and a group of alien rebels are at war, with humanity caught in the middle. The episode features intense action scenes, including a confrontation with the Smoking Man, and ends with Mulder's realization that his beliefs may have been manipulated by those behind the conspiracy.

    This episode was intended as the season finale but was extended due to network demand. The alien rebel, a recurring element, was introduced here, altering the course of the series' mythology.

    "Two Fathers" (Season 6, Episode 11)

    The episode reveals much of the series' overarching conspiracy, focusing on the Syndicate's collaboration with aliens to create a human-alien hybrid. Mulder and Scully investigate the disappearance of a group of scientists involved in these experiments. The Smoking Man is revealed to be Mulder's father, deepening the personal stakes for Mulder. The episode ends with the destruction of the Syndicate by the alien rebels.

    This episode was the first to feature Mulder's new informant, "X." It also serves as a critical turning point in the series, revealing key details about the Syndicate's plans and its ultimate downfall.

    "One Son" (Season 6, Episode 12)

    Following "Two Fathers," Mulder and Scully continue to unravel the conspiracy. They learn that the alien colonists plan to take over Earth, and the Syndicate has been aiding them in exchange for their own survival. Mulder confronts the Smoking Man, leading to a dramatic showdown. The episode ends with the apparent destruction of the Syndicate, but the alien threat remains.

    The episode marks the final appearance of Jeffrey Spender, a key character in the mythology arc. It also features the first on-screen confirmation that the Smoking Man is Mulder's biological father.

    "Requiem" (Season 7, Episode 22)

    Mulder and Scully return to Bellefleur, Oregon, the site of their first case, to investigate strange phenomena. Mulder is abducted by aliens during the investigation, and Scully discovers she is pregnant under mysterious circumstances. The episode revisits the show's roots while setting the stage for major changes in the characters' lives.

    Last episode to feature David Duchovny as a regular cast member, though he would appear in guest roles. The pregnancy storyline would become a central element in the following seasons.

    "Within" (Season 8, Episode 1)

    Scully, now working without Mulder, searches for her missing partner while facing new challenges within the FBI. She encounters John Doggett, a new agent assigned to find Mulder. The episode introduces the "Super Soldiers," a new alien-human hybrid threat, and sets the tone for the series' shift in focus with Mulder's absence.

    This episode marks the first appearance of Robert Patrick as John Doggett. The introduction of the "Super Soldiers" was part of the series' effort to refresh the mythology with new elements.

    "The Truth" (Season 9, Episode 19/20)

    In the two-part series finale, Mulder is on trial for the murder of a military officer, a charge tied to his investigation of the alien conspiracy. As he and Scully try to uncover the truth, they encounter old allies and enemies, leading to a climactic confrontation with the Smoking Man. The series ends with Mulder and Scully on the run, determined to continue their quest for the truth.

    The finale attempts to tie up many of the series' loose ends. It was the last episode to feature Gillian Anderson as Dana Scully until the show's revival in 2016. The Smoking Man is seemingly killed off in this episode, though he would return in the revival seasons.

    "My Struggle" (Season 10, Episode 1)

    In the revival's first episode, Mulder and Scully reunite to investigate a new conspiracy involving government cover-ups and the alien invasion. The episode modernizes the show's mythology, introducing new threats and revisiting old ones. Mulder becomes obsessed with exposing the truth, while Scully grapples with the implications of their findings on her own life.

    This episode was the first new X-Files episode in over 13 years, watched by over 16 million viewers. It was intended to bring the series' themes into the 21st century, reflecting contemporary issues like government surveillance and genetic experimentation.

    "Founder's Mutation" (Season 10, Episode 2)

    Mulder and Scully investigate the mysterious death of a scientist involved in genetic experiments. They uncover a corporation's involvement in creating genetically modified children with extraordinary abilities. The case triggers personal memories for both Mulder and Scully, especially concerning their son, William. The episode blends classic X-Files themes with modern scientific fears.

    Directed by James Wong, who wrote several classic episodes of the original series. The episode received praise for its exploration of the emotional toll on Mulder and Scully due to their past decisions, particularly regarding their son.

    "My Struggle II" (Season 10, Episode 6)

    In the season finale, Mulder and Scully race against time to stop a global pandemic unleashed by the alien conspiracy. The episode features a dramatic confrontation with the Smoking Man and ends on a cliffhanger, with Mulder's life hanging in the balance and Scully making a shocking discovery about her own biology.

    Originally intended as the series finale, this episode's cliffhanger led to fan outcry, resulting in the show's renewal for an 11th season. The episode heavily draws on themes of bioterrorism and government complicity, resonating with contemporary fears.

    "Mythology Arc" (Season 11, Episodes 1-4)

    Mulder and Scully continue their pursuit of the truth, encountering new threats and old enemies in a world that has become even more dangerous. The arc explores the deepening conspiracy, including the involvement of global elites in the alien agenda and the growing threat of the "Super Soldiers." The episodes build towards a final confrontation that could determine the fate of humanity.

    Written by Chris Carter, these episodes feature the return of several classic characters, including Skinner and the Smoking Man. The arc reflects the show's evolution, incorporating contemporary issues like climate change and political corruption into its mythology.

    "My Struggle IV" (Season 11, Episode 10)

    In what was intended to be the series finale, Mulder and Scully face off against the Smoking Man and other conspirators in a desperate attempt to prevent a global catastrophe. The episode delivers answers to long-standing questions about their son William and the true nature of the conspiracy. The episode ends with Mulder and Scully surviving but left to face an uncertain future.

    The episode was initially planned as the final episode of The X-Files, bringing closure to many of the series' ongoing storylines. It features the return of several classic characters and is notable for its fast-paced narrative, attempting to resolve decades of storytelling in a single episode.


    gillian anderson red dress rollingston
    It's an X-File itself why this image is in this post...



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My name is Jimmy Jangles, the founder of The Astromech. I have always been fascinated by the world of science fiction, especially the Star Wars universe, and I created this website to share my love for it with fellow fans.

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