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Series in general
- Chris Carter named Scully for longtime Los Angeles Dodgers broadcaster Vin Scully. In "Irresistible" a character says something like "Scully. Like that baseball announcer."
- Agent Doggett is named for Vin Scully's longtime partner in the booth, Jerry Doggett.
- Mulder's apartment number (42) is perfect for a man obsessed with aliens and the search for ultimate truth.
- The numbers "1013" and "1121" show up frequently as case files and time-stamps, which correspond to Chris Carter's birthday and his wife's respectively. Mulder's birthday is also October 13.
- In the 2016 revival episode "Mulder and Scully and the Were-Monster," the Monster of the Week dresses exactly like Carl Kolchak.
- The Monster of the Week in the revival episode "Home Again" kills several people via spine-rip fatality.
The X-Files Game
- Craig Willmore’s love interest and supporting character Detective Mary Astadourian is named after the vice president Mary Astadourian, the chief researcher and office manager of the company Ten Thirteen Productions that produces the show as well as Chris Carter’s personal assistant.
- Shady character James Wong is named for staff writer James Wong of seasons one, two and four.
- Late in the game, Craig Willmore gets an e-mail from a “Monte Joffin,” John Joffin is the director of photography for the game and even worked for the series.
- Craig lives at Eavelyn Apartments, named after Halle Eavelyn the executive producer of the game.
- One of the flyers on the board in the FBI Conference Room advertises “Yoga – Instructed by David,” a homage to David Duchovny, Mulder’s actor who practices yoga.
- The Town of Charno is named after staff writer Sarah Charno during season two.
- Gordon’s Hauling is possibly named for writer Howard Gordon.
- When any of the televisions are turned on, a short clip from Riot Squad is shown.
- Craig Willmore asks if he got those prints lifted:
John Amis: Ah jes' fished |em, Miss Daisy, ah still needa process’m.
- Mary mentions The Twilight Zone.
- John Amis quips a famous line from Star Trek: The Next Generation.
- Mulder mentions he always wanted to visited Canada.
- Upon meeting Mr. X for the first time:
Craig: So you’re the mystery man. I was expecting someone a little more Sean Connery.
- John Amis imitates Sean Connery’s voice when talking to Craig.
- One of the items collected from Mulder’s room is fictional book From Outer Space by Jose Chung.
- Richard Langly asks if Craig wants Attorney General of the United States Janet Reno’s number.
- Richard Langly’s nickname is “Ringo” as in Ringo Starr, John Ringo and Shiina Ringo
- Mark Cook calls Craig Golden Boy after the latter tells the former FBI Agent Armistead Shanks to hand his current case to Cook.
The X-Files: Fight the Future
- The bomb at the start has been frequently likened to real life Oklahoma City bombing of 1995.
- Working title for this movie was “Blackwood,” coming from the works of English writer Algernon Blackwood.
- After consuming much alcohol and finding the bar’s bathroom locked, Mulder decides to relieve himself on a wall displaying the Independence Day poster in the alley.
- To Byers, Langly and Frohike the Three Gunmen:
Mulder: Oh my god. Cowardly Lion, Scarecrow, Toto!
- A similar shaped space ship like the one from The Thing is found buried in ice at Antarctica.
- Conrad Strughold was named after Nazi scientist Hubertus Strughold who conducted experiments on prisoners during World War II.
- The newspaper article titled “Fatal Hanta Virus Outbreak in Northern Texas Reported Contained” Mulder reads at the end of the film was written by reporter Howard Dimsdale, the name of the teacher who taught writers Frank Spotnitz and John Shiban ath the American Film Institute.
- The scene which Scully and Mulder are chased through a cornfield by helicopters in a reference to a famous “crop duster” scene.
- Stevie is named after one Chris Carter’s boyhood friends.
- A New Hope, Close Encounters of the Third Kind, Apocalypse Now, Alien, The Empire Strikes Back, Raiders of the Lost Ark, Spies Like Us and Miss Smilla’s Feeling for Snow are either referenced or parodied.
The X-Files: Resist or Serve
- In the opening, Scully is explaining that a bunch of high school girls have fascinations with witchcraft doesn’t mean they’re raising the dead:
Mulder: Saw them do it on Buffy.
- The name of a biotechnology company, "Rauch", was used before as a villain's name.
- There’s a villain named John Gillnitz, a combination of the names of series writers John Shiban, Vince Gilligan and Frank Spotnitz.
- There’s a gas station called Holly’s, after Vince Gilligan’s girlfriend, Lucy “Holly” Hartwell Rice.
- There is a sign advertising Morley Cigarettes, a fictional brand that appears not only through this series but in 24, Becker, Broken Saints, Cold Case, The Dick Van Dyke Show, ER, Friends, Jake 2.0, The L Word, Mannix, Mission: Impossible, Murder in the First, The Outer Limits, Space: Above and Beyond, Spy Game That '70s Show, The Twilight Zone, 200 Cigarettes, Beverly Hills, 90210, Buffy the Vampire Slayer, Dan August, Epicenter, Freddy Got Fingered, Gun Shy, Judging Amy, Malcolm in the Middle, Millennium, Murderer’s Row, Nash Bridges, Prozac Nation, Special Unit 2, System Shock 2 and Thirteen.
- The image on one of the monitors strongly resembles a green Fight the Future poster.
- Frohike says a variant of 'open sesame' by saying “Open says-me!”
The X-Files: I Want to Believe
- Mulder visits the Nutter feed store, last name of David Nutter who directed many episodes.
- Franz Tomczeszyn shares the same surname as costume designer Lisa Tomszeszyn.
- Title sequence of The Jeffersons is shown on television in a dorm.
- When Mulder tries calling Scully from his cell phone, the display shows two names above and one name below hers:
- Bowman is a director Rob Bowman who directed the first movie and several episodes
- Gilligan refers to a writer and producer Vince Gilligan of the show.
- Shiban is John Shiban, another writer and producer.
- When Mulder and Scully are talking in bed, the book lying next to Scully’s pillow is Beautiful WASPs Having Sex by Dori Carter, Chris Carter’s wife.
- When Scully first visits Mulder in his rural home, he is tacking up a story titled ‘Princeton Closes ESP Lab after 40 Years of Paranormal Study,’ a real life event where the 'Princeton Engineering Anomalies Research (PEAR) facility' closed in 2007 after school administrators felt continued funding was unjustified, after failing to provide conclusive evidence of what they were doing could happen, large scale experiments showed a statistically detectable influence. The lab's original mission was to investigate possible phenomena for the defense industry, such as if the minor electrical field present in the human body could interfere with sensitive electrical equipment when the body was placed under extreme stress.
- Special Agent Mosley Drummy mentions E.T. abducting Mulder’s sister.
- As depicted in the film, head transplants have actually been legitimately performed on monkeys, and head reattachment is actually being considered as medical procedure.
- After being rescued, Mulder tells Skinner “Cold, I’m cold”, to which Skinner holds him in his lap, whereas Mulder did the same thing for Scully.