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.
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.
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.
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 WAS Ps 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.