X-Files Retrospective: How Vince Gilligan Came Up With The Best Final Episode for the Series — Twice

David B Morris
12 min readAug 1, 2024

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If Only Chris Carter Had Listened

Vince Gilligan was the happy, fun guy on the X-Files. Seriously!

Any shortlist of the greatest showrunners of this century has to have Vince Gilligan on it. It is not just because he created two of the greatest series of all time — Breaking Bad and its prequel Better Call Saul — but because in an era where the series finale matters more than it ever did, Gilligan and his writers managed to stick the landing not once, but twice. Its not just that for many viewers the series’ finales for both shows are clearly among the best in history but because the entire final season for both shows led up to it perfectly every step of the way. With the exception of David Simon, who managed to perfectly close out not only The Wire but his follow-up HBO series Treme and The Deuce I don’t know of any showrunner who has that great a track record.

As I’ve mentioned in an earlier entry Gilligan cut his teeth working for The X-Files writing his first script in 1995, becoming a staff writer in Season 4 and staying with the series until the final season. Only his colleague Frank Spotnitz, who also joined the series in Season 2, stayed with the show for nearly as long and anyone who looks at Gilligan’s writing over the course of the series knows that he was not only the superior but far more consistent writer. Gilligan wrote or collaborated on 30 different episodes and the majority of the episodes he wrote were among the greatest in series’ history.

Like Darin Morgan, Gilligan was the great comic genius of The X-Files but while both were brilliant satiric writers, Gilligan’s scripts had a different kind of humor than Morgan’s. Morgan’s satiric style was meta and had a much darker humor to it: as much as one laughs at Clyde Bruckman and Jose Chung, there’s a melancholy tone along with so many of the great jokes. Gilligan is essentially a more optimistic writer not only then Morgan but overall. And Gilligan didn’t have an outsiders look; he wanted to joke at it from within.

We see this in some of the greatest comic episodes he wrote over the years; not just Small Potatoes which looks at our great hero Mulder and shows that he himself is something of a loser, but other superb gems over the years. Among his crowning achievements were two masterpieces in Season 5: Bad Blood in which he radically reinvents the format of the show to see how Mulder and Scully see each other and Folie A Deux, which shows that Mulder and Scully are soulmates, because they have a common insanity. Gilligan also had a gift of creating some of the most human monsters-of-the-week of the entire canon, some of which make you wonder about just so much of what Mulder and Scully doing. In Bad Blood, Mulder and Scully discover what seems to be an entire small town of vampires and learn through the wonderful sheriff (Luke Wilson) that the vampires are average citizens who don’t want to be spotted. “We pay our taxes,” Wilson’s character says at one point. Gilligan had a gift with so many of his monsters to make their superhuman abilities actually make them more ordinary. This led to the inevitable conclusion in Season 7 masterpiece Hungry which took place entirely from the perspective of the monster and went out of its way to make Mulder looking like a man toying with his prey to the point he almost seemed a villain.

When the series began its decline in the seventh season Gilligan was the only writer on the show still capable of turning out masterpieces on a regular basis. During Season 7, he not only wrote the exceptional Hungry but the wonderful X-Cops which found Mulder and Scully interacting with the Fox hit series. Filmed entirely on video and playing like an actual episode of the series it was one of the comic highpoints of the entire show: not only because it showed Mulder eager to have an X-File play out on live TV but because it showed the bold and fearless Scully understandably terrified that her eager partner was going to embarrass them on TV — and seemed incredibly reluctant to ever appear on camera.

It remains unclear if Season 7 was going to be the last one when it was being filmed but Gilligan may have very well thought it would. Writing what many thought at the time would be the penultimate episode of the series Gilligan also got to realize his dream of making his directorial debut. And if it was going to be the final monster of the week, Gilligan pulled out the stops.

Je Souhaite deals with Mulder and Scully investigating a series of ‘crimes’ by the Stokes’s brothers, played by those brilliant comic geniuses Kevin Weisman and Will Sasso. (Weisman was a year out of becoming famous for his work on Alias; Sasso had become one of the breakout sensations of the late night comedy MAD TV.)

Gilligan usually treats most of the characters in his stories wit respect and love, even the monsters, but with the Stokes brothers he goes out of his way to show them as among the dumbest people possible. The gimmick of the episode is that Anson discovered a genie in a rug and has become its master. He is granted three wishes and its clear he is incapable of making good ones. His second wish is for a giant boat but because he didn’t specify it was in the ocean, it’s parked outside his house. There’s also the fact his brother Leslie is in a wheelchair, thanks to an accident of stupidity years earlier. The genie suggested to Anson what the right thing to do is — but neither Anson nor Leslie seem able to see the logic.

Anson’s third wish involves something that should bring money. The genie (Paula Sorge) makes sardonic suggestions he might want to wish for intelligence or talent and Anson thinks he should wish for a money machine. Finally he asks to turn invisible at will. The genie rolls her eyes, tells him his wish is breathtaking in its unoriginality, but grants it. Anson walks out on to the street turns invisible — and is promptly flattened by a truck when he sets his eyes on a pretty girl.

Scully couldn’t believe her eyes…for most of the episode, anyway.

The body turns up at the morgue — and Scully’s eyes practically bug out as she first realizes that its invisible and then seems genuinely in awe. (When she puts the body back in the freezer, she says ‘Bye’ in a girlish fashion. By this point Mulder has come to realize the Stokes brothers have found a genie and this genie has a long history. Using the national archives he finds images of the genie with Mussolini and Richard Nixon. (That would explain a lot.) Mulder goes to see Leslie, who is still staggering — and has to hear the theme to I Dream of Jeannie to know what a genie is.

Leslie then gets the rug back and once again the genie suggests the obvious. Leslie considers this. “Oh, a solid gold wheelchair.” His first wish is to ask for his brother to come back from the dead. By this time Scully has called in a bunch of scientists to see her discovery — and her face falls flat when she finds the compartment empty.

It has now become very clear that bring Anson back from the dead was a horrible idea, and Anson makes it very clear. Leslie has just figured out to wish for ‘legs’ — just as Anson lights a match to explode the gas in the trailer, blowing both him and his brother up to kingdom come.

Mulder and Scully now find themselves with the genie, who seems remarkably non-plussed to see them. She’s been a genie for more than five hundred years and she is appropriately cynical, saying that mankind has not changed for five hundred years. “They always make the wrong wish,” she says. They are about to move on when the genie tells Mulder that since he unrolled the rug he gets three wishes.

Mulder wants to do the right thing — he wants to make a selfless, completely free-of-obligations wish. (Considering everything he’s gone through the past seven years; you might think he’d want the conspiracy explained to him but that’s never been Gilligan’s style anyway.) So he wishes for peace on earth. The genie grants it. Immediately after it happens, Mulder’s face falls. He runs outside — and finds that the streets are empty of people. “I should have known you’d do this!” he shouts, running to the Bureau. Naturally his next wish is to reverse the first wish and he begins to lecture the genie — right as Skinner reappears.

In the final minutes Mulder is in the middle of writing out the details for what he believes the perfect wish will be. Scully shows up in his office. “You don’t remember disappearing for about an hour earlier today?” Mulder asks Scully. Scully doesn’t.

Mulder tells Scully what’s he planning to do — make the kind of wish that will make the world a perfect place. Scully tells him if you do that, what is the point of our everyday existence? Now this seems to go against the nature of so much of the series message, particularly the mythology, but Gilligan has a bigger point that argues that at the end of the day The X-Files was never about solving the big problems but the relationship we’d found with the characters we love. Mulder listens turns off the computer and makes his final wish.

In the final scene Mulder and Scully are about to watch Caddyshack. (“I can’t believe you’ve never seen that,” he tells her.) He mentions to Scully that: “I don’t know if you noticed, but I never made the world a happier place,” he tells her. “Well, I’m happy,” Scully says. “That should count for something. What was your third wish?” she asked. Mulder smiles.

In the final scene we see the genie drinking a coffee and with the mark of the djinn gone. There’s a smile on her face we haven’t seen the entire episode. Someone finally made the right wish.

The episode is, as one reviewer called it, “a note of perfect bliss” and had it been the final monster of the week, it would have a great triumph for the series. Then of course came Requiem — and the decision was made to keep the show going.

Gilligan’s role in the final two seasons of the series was significantly smaller; during Season 8 The Lone Gunmen spinoff which had been a development hell for years was finally greenlit by Fox and he took on the role of showrunner. He only wrote one script for season 8 but it was a gem: ‘Roadrunners’, a brilliant piece of body horror where a cult in a small desert town worship a slug as God and have a habit of stoning people to death for the next host. Scully ends up discovering the town, becomes a prisoner and becomes a host.

The show is one of the great works of horror for the series and Gillian Anderson gives one of her best performances of the final two seasons in it, playing someone desperately lost and increasingly aware of how trapped she is.

When The Lone Gunmen died a quick death Gilligan returned for Season 9. Gilligan wrote two solo scripts and one shared credit. The shared credit ‘Jump The Shark’ revisited The Lone Gunmen after their series ended and is considered one of the worst episodes in the series. However John Doe, an episode where John Doggett (Robert Patrick) wakes up with amnesia in a town in Mexico is one of the classics of the final seasons, a brilliantly dark scripted series where Doggett has to realize his identity — by learning that his young son is dead. Patrick gives one of his best performances in the series.

By the time that episode aired it was known the series was cancelled. Gilligan was once again allowed to write and direct what was definitely going to be the last monster of the week episode. Sunshine Days was not quite at the level of Je Souhaite but it had a level of brilliant meta commentary, great humor and once again gave a clear message as to what The X-Files had really been about.

Things are going to get weird in the Brady Bunch House.

Doggett and Reyes are called into investigating a strange death of a young man who died in what the neighborhood called ‘The Brady Bunch house’. These two young men (one of them played by David Faustino) are flown through the air in telekinesis and killed.

The owner of the house is known as an Oliver Martin (Michael Emerson cast very against type from the kind of character he has played basically his entire career on TV.)Reyes does some research — on a Brady Bunch website — and finds out this is the name of ‘Cousin Oliver’, the character who was written on The Brady Bunch in the final season.

Gilligan has never done anything quite so meta in his career. This is the story of a man fixated on a popular TV show, so lonely he derives comfort from its presence around him.(He constantly recreates the family in the house.) He’s taken on the identity of a forgotten late edition to the cast when it was nearing cancellation. (Again Reyes is the one to figure it out, which is meta.) And the dilemma he faces is whether he can find a way to live without it, because a constant exposure to the fantasy is killing him.

Oliver as a child possessed a kind of psychokinesis that enables his thoughts to become reality. Scully learns about this and mentions that they need to find proof. “I’ve investigated 200 cases” she tells Doggett and Reyes — the exact number of episodes.

What’s particularly remarkable about Gilligan’s work on The X-Files — particularly for the man who created Walter White — is that at his core he was a humanist who sees there are always more important things to care about then government conspiracies. This stands in contrast to the series finale where Mulder chooses to sacrifice his happiness with Scully to uncover the same truth he’s been chasing all his life. By contrast Gilligan argues all of this is bunk.

Scully finally gets the proof she’s been searching for all her life. She’s planning to get a Nobel Prize. Witnessing it Skinner says joyously: “With this, The X-Files can go on forever!” And then as Oliver begins to decline physically because of his use of the power, they face a darker question.

Doggett realizes the truth. He talks to the doctor who first observed Oliver (John Aylward) who tells him that he spent weeks with him but the longer he stayed the more his power diminished. The doctor realizes why. “For the first time in his life, he was happy.” Doggett realizes that the way keep Martin alive is for the doctor to keep being his surrogate father. In the final scene he agrees to do so — on the condition he never uses his power again.

Scully walks away from this not dismayed but happy. One of the final scenes shows that Doggett is started to enjoy these cases and that Scully has finally learned her lesson

Gilligan also takes a shot at the mythology in this storyline. Oliver has the ability to make objects float, he’s the kid who can change the world — in other words, this is exactly everything we’ve been dealing with Baby William all season. Gilligan’s solution is to show that love matters to keep a child safe — William, by contrast, was injected with a bit of metal (that didn’t even work, according to the revival.)

Sunshine Days is nowhere near the level of Je Souhaite or indeed Gilligan’s best work (he did set the bar very high) But in both of those scripts Gilligan demonstrated that the best way to end a series like The X-Files was not with a huge information dump or revelations about a conspiracy but to remind us that it was about the journey you took and the people you met along the way. (This is close to the ending Gilligan would give us for Better Call Saul, if not Breaking Bad.)

When the series was revived in 2016 and again in 2018 Gilligan wasn’t among the former writers to return to The X-Files. (To be fair, he was very busy at the time.) But I honestly don’t think he needed to come back to the show, though it would have been nice if he had. Gilligan had made his point about what The X-Files was really about in what might have been the penultimate episode and the actual penultimate episode. And honestly given how the revival played out, there’s a good chance given the final episodes that Gilligan’s message, if not the execution, finally registered with Carter and his colleagues. What more did he need to say?

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David B Morris

After years of laboring for love in my blog on TV, I have decided to expand my horizons by blogging about my great love to a new and hopefully wider field.