When *The X-Files* first premiered back in 1993, few could have predicted the cultural phenomenon that Chris Carter had created. David Duchovny and Gillian Anderson quickly became household names as audiences tuned in to Fox every Friday night (and later Sunday) to follow the strange and impossible cases of FBI agents Fox Mulder and Dana Scully. From UFO sightings and alien abductions to demonic schoolteachers and parasitic monsters lurking in the sewers, there was nothing too weird, outlandish, or macabre for this duo. For nearly a decade, the show ran uninterrupted on the network, captivating viewers with its unique blend of sci-fi, horror, and mystery.
Fast forward to today, in an era where Ryan Coogler may be rebooting *The X-Files*, it’s worth reflecting on the original series along with its two feature films and the revival seasons that aired between 2016 and 2018. One wonders: did the show ever truly wrap everything up? In classic *X-Files* fashion, plenty of mysteries and plotlines were left unresolved. The mythology in particular still contains significant gaps, and many storylines never earned satisfying conclusions. Some characters and events simply faded into obscurity, forgotten when the show came to a close.
If you’re anything like us, you likely still believe the truth is out there. Unfortunately, *The X-Files* never concluded with a grand, spectacular finale that tied up every loose end. With that in mind, here are some of the storylines we wish had received better closure or at least a more thorough explanation.
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### The 2012 Alien Invasion That Never Happened
In the original series finale, Season 9’s two-part episode *“The Truth”*, Mulder is court-martialed after a season-long absence during which he uncovers the truth about a global alien conspiracy. He learns that the Syndicate’s collaboration with the alien Colonists was set to culminate in a full-scale invasion by December 2012, coinciding with the end of the Mayan calendar.
When this aired in 2002, the prospect of an alien invasion a decade later felt ominously possible. However, the 2008 film *The X-Files: I Want to Believe* did not address those invasion plans, leaving fans hoping for a third movie to tackle the event. Instead, the fateful date came and went without incident.
By the time the series returned in 2016, the 2012 deadline was casually brushed aside as an issue of “climate change.” In the Season 11 premiere, *“My Struggle III”*, Mulder and Scully discover that due to Earth’s depleting resources, the aliens abandoned plans for colonization. Yet, confusingly, the Cigarette Smoking Man (William B. Davis), also known as CSM, is still working on a depopulation project linked to continuing invasion efforts.
This muddled explanation is a prime example of *The X-Files* beginning a storyline it never fully delivered on. Fans were left wishing the series had found a more creative way to handle the 2012 invasion—for instance, perhaps the black oil virus might have re-emerged unexpectedly, or the aliens needed to buy more time. But none of that happened. Maybe the reboot will finally bring clarity.
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### The Replaced Agents Who Were Never Replaced
Throughout the show’s run, there were multiple moments when Mulder and Scully seemed on the brink of being replaced. While Duchovny and Anderson are undeniably the definitive paranormal FBI duo, David Duchovny stepped back from the show in later seasons. Despite rumors he had left for good, Duchovny continued to appear sporadically in over a dozen episodes before the initial run ended.
In his absence, Robert Patrick’s Agent John Doggett was introduced to fill Mulder’s role. The final two seasons gradually phased out Mulder and Scully from fieldwork, pushing Doggett and Monica Reyes (Annabeth Gish) to the forefront. Though no Mulder and Scully, Doggett and Reyes formed a competent team, hinting that *The X-Files* could continue without its iconic leads.
However, when the series returned in 2016, Doggett and Reyes were mostly left behind. New agents Kyd Miller (Robbie Amell) and Liz Einstein (Lauren Ambrose) emerged as the new “Next Generation.” Yet, just like their predecessors, these characters were quickly sidelined and eventually discarded.
Despite multiple attempts to expand the X-Files Division beyond Mulder and Scully, none of these successors ever stuck. To this day, Doggett’s fate remains unknown, and Reyes’ abrupt downfall in Season 11 was deeply disappointing. Like many characters introduced over the years, the replacements were either forgotten or misused.
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### The Disappointing Fate of Samantha Mulder
From the very beginning, Mulder’s quest for the truth was deeply personal—rooted in the abduction of his sister Samantha as a child. This traumatic event drove him toward his career in the X-Files. Yet, while Samantha was a major plot point early on, it became clear the show struggled with how to resolve her storyline.
Numerous clones and replicas of Samantha were introduced, many claiming to be “the real one,” but Mulder never reunited with his actual sister. Instead, Season 7’s *“Closure”* reveals that Samantha had been dead for years. The truth was discouraging: she was taken by the Syndicate to a new home, raised alongside her half-brother Jeffrey Spender by the CSM, abducted repeatedly, and ultimately died.
This ending was strange and underwhelming after such an emotionally charged lifelong search. While it provided Mulder with some semblance of closure, it left many fans—and arguably Mulder himself—unsatisfied. Even years later in *I Want to Believe*, Mulder continued wrestling with his inability to save her. It’s a prime example of a powerful story that lacked a fitting conclusion.
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### The Vanished Alien Rebels
By Season 5, the show began introducing various alien factions, among which the faceless “Alien Rebels” were particularly intriguing. These aliens opposed the Colonists’ plans for domination and had deliberately avoided contraction by the black oil virus that enslaved most of their species.
However, the Alien Rebels appeared only a handful of times before vanishing entirely. The original series finale *“The Truth”* claimed the Rebels had killed all Syndicate members except the CSM back in Season 6, but subsequent seasons contradicted this.
Their absence was puzzling, especially as the conspiracy shifted toward the Season 9 Super Soldier storyline. Why didn’t the Rebels continue opposing the Colonists’ plans? Season 10 compounded the confusion by revealing the Alien Rebels were, in fact, a hoax designed to distract Mulder from the true conspiracy: human depopulation.
Not only were the Rebels removed as a key plot device, but their retconning felt like a huge missed opportunity. Rather than building on their presence, the revival instead dismissed them without offering clear answers.
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### The Underused Nanobot Plot and Alex Krycek
In Season 6’s *“SR-819,”* Alex Krycek (Nicholas Lea) poisons Assistant Director Walter Skinner to infiltrate the FBI and spy on Mulder and Scully. Krycek’s cryptic reply—“All in good time”—builds suspense around his goals.
Yet, this plotline falls flat. Krycek’s main “victory” is having Skinner secretly record the agents, which has little impact. Krycek’s character was infamous for being a “wasted potential” villain—each time he seemed crucial, he was left for dead or sidelined in Russia with his arm sawed off.
The nanovirus poisoning was similarly a swing and a miss. It could have provided Krycek with major leverage over Skinner and the X-Files Division but instead fizzled out quickly when Krycek was imprisoned in Tunisia. When Krycek later returns in Season 8, he blackmails Skinner to prevent Scully’s baby from being born. Ultimately, Skinner shoots Krycek dead in *“Existence.”*
To date, the nanobots remain in Skinner’s system, yet the revival seasons never used this as a plot point or bargaining chip. This oversight is frustrating given the potential for deeper intrigue involving Skinner’s compromised condition.
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### The Tragic and Forgotten Emily Sim
Early in the series, Scully is abducted and learns her ova were stolen, leaving her unable to conceive naturally. In a heartfelt two-part holiday arc in Season 5 (*“Christmas Carol”* and *“Emily”*), it’s revealed that her stolen ova were used to create Emily Sim—a young girl who is biologically Scully’s daughter.
Scully is conflicted but vows to raise Emily as her own. Tragically, Emily falls ill when she misses her Syndicate treatments and eventually dies. Scully is forced to bury her shortly after meeting her.
This deeply emotional and traumatic storyline is notably dropped afterward. Emily is mentioned briefly in hallucinations but disappears from the narrative. When Scully discovers Emily’s casket is empty and her body removed as evidence, the trail goes cold.
Given the show’s early introduction of clones and replicated children—as with Mulder’s sister Samantha—it seems likely that other Syndicate-made children could exist. Yet the series abandons this thread entirely, pivoting instead to the introducing of William’s storyline in Season 8.
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### The Millennium Crossover That Never Finished
Here’s a bit of a cheat, but since the TV series *Millennium* technically concluded with an *X-Files* crossover episode, it deserves mention.
*Millennium* followed former FBI profiler Frank Black (Lance Henriksen) investigating cases tied to the ominous Millennium Group—a shadowy organization with apocalyptic plans. Though cancelled after three seasons, its story ended right before the year 2000. To wrap up its plot, *The X-Files* brought Frank back in Season 7.
We learned that a group member planned to use resurrected “Four Horsemen of the Apocalypse” to bring about the end of the world on New Year’s Eve. However, this storyline was convoluted and left ambiguous, with unclear outcomes regarding whether Mulder, Scully, and Frank successfully stopped the Group.
*Millennium* fans have awaited more closure. In 2015, IDW Publishing released a five-part comic series titled *Millennium*—in which Frank Black teams up with Mulder to battle the Group. While not official canon, the comic highlights how the show never fully completed the story arc, leaving room for further exploration.
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### The Letdown That Was William Scully
Perhaps the biggest disappointment in *The X-Files* saga is the treatment of William Scully, the boy later known as Jackson Van De Kamp (Miles Robbins).
Scully’s pregnancy was teased at the end of Season 7, with much of Season 8 focusing on William’s birth. Debate swirled around whether his conception was miraculous (as Season 8’s *“Essence”* suggests) or engineered by the Smoking Man (as claimed in Season 11’s *“My Struggle III”*).
William was portrayed as a human-alien hybrid destined to be the next evolutionary step, a symbol of hope amid the Colonists’ plans for a new world order. Various factions, including the Season 9 cult in *“Providence”*, believed he would be central to the future.
Yet when the revival arrived, William’s significance was drastically diminished. Although he survived being shot by the CSM in *“My Struggle IV,”* he goes into hiding and is largely forgotten by his parents, who instead focus on a new child Scully conceives.
This abrupt sidelining is frustrating. The last four seasons seemed poised to explore William as the bridge between species to save humanity from the alien Spartan virus. Instead, the show moved on at the earliest opportunity—a profound letdown for fans invested in the mythology.
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### Is Dana Scully Immortal?
One of the series’ most intriguing but least explored ideas is whether Dana Scully is immortal.
The revival seasons even poke fun at this notion in *“Mulder and Scully Meet the Were-Monster,”* but for the most part, the show leaves this question open-ended.
The idea arises as early as Season 3’s *“Clyde Bruckman’s Final Repose”* when Bruckman—who can foresee death—tells Scully bluntly, “You don’t [die].” The following season, she acquires an ouroboros tattoo, a symbol connected to immortality and the Millennium Group.
In Season 6’s *“Tithonus,”* Scully is saved by Alfred Fellig, a man with over 200 years of life who gives up his extended lifespan to her. Mulder theorizes that Fellig’s immortality was transferred to Scully.
Fans have speculated wildly—some crediting the Syndicate chip in her neck (which cured her cancer), others her Catholic faith and spiritual “eternal life.” Yet *The X-Files* never offers definitive answers, leaving room for interpretation.
If Scully is truly immortal, it would explain why she repeatedly escapes death. Still, the show maintains the tension surrounding her safety, giving the idea a haunting, unresolved quality.
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### The Forgotten Tragedy of Gibson Praise
Easily the most overlooked storyline in *The X-Files* involves Gibson Praise, played by Jeff Gulka. Gibson is a young boy with alien DNA, granting him mind-reading abilities. Pursued relentlessly by the Syndicate, Gibson goes into hiding.
He reappears during Mulder’s court-martial in *“The Truth”*, where his heroic testimony serves as some of the strongest evidence of alien activity and governmental conspiracy. But after that pivotal moment, Gibson disappears from the story entirely.
Gibson Praise represents perhaps the best tangible proof Mulder and Scully ever had. Yet, his post-Season 9 fate is never addressed. Though John Doggett vows to protect him, the show offers no reassurance that the Syndicate didn’t catch up to Gibson later.
Interestingly, the IDW *X-Files* comics by Joe Harris revive Gibson’s character—though outside of canon—portraying him as a supervillain desperate to connect with the Colonists and carry out the Syndicate’s plans. This darker take underscores how much narrative potential the show left unrealized by abandoning his storyline.
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### Final Thoughts
*The X-Files* remains one of television’s most iconic sci-fi mysteries, boasting some of the most enduring characters and stories in genre history. Yet it’s undeniable that many key plotlines and characters were left dangling or abandoned, leaving fans with lingering questions and unresolved mysteries.
Whether it’s the missed 2012 invasion, the mishandled William storyline, or the disappearance of vital characters like Gibson Praise and Emily Sim, the show’s sprawling mythology often felt like a never-fully-answered puzzle.
With the possibility of a reboot on the horizon, fans can hope that these loose ends might finally be addressed, and that the quest for truth will continue with fresh eyes and renewed purpose. Until then, the legacy of Mulder and Scully—and their unanswered questions—will remain very much out there.
https://www.looper.com/2012466/the-x-files-storylines-never-paid-off/
