According to writer Robert Engels, he and director David Lynch originally conceived this film as the first in a series of films exploring the mythology of the Black Lodge. To that effect, the two inserted four characters as "outs" with which to continue the story: Agent Dale Cooper (Kyle MacLachlan), Agent Phillip Jeffries (David Bowie), Major Garland Briggs (Don S. Davis) and Agent Chester Desmond (Chris Isaak). The critical and box-office failure of this film, however, caused Lynch to abandon any plans for sequels.
The song "Sycamore Trees" featured in Twin Peaks: Episode #2.22 (1991), but appearing on the movie soundtrack, is claimed by Norwegian pop group A-Ha to be an unauthorized cover of their song "Sycamore Leaves" written in 1989. A-Ha band member Pål Waaktaar sued David Lynch (Lynch wrote the lyrics for Sycamore Trees) for plagiarizing, but eventually lost the case.
Richard Beymer (Ben Horne) declined to participate due to a scene where Ben was to force Laura to kiss him in exchange for a bag of cocaine. Beymer felt that there had been no buildup for the character of Horne (who confesses his love for Laura in Twin Peaks (1990)) to extort Laura, and that as a result the scene came off as exploitative. As a result, another scene, in which Leland Palmer (Ray Wise) confronts Ben about Laura's photo being on Ben's desk, resulting in a fight with Ben's wife, was never shot. The scene also would have included Johnny and Jerry Horne.
In most versions of the film certain sequences are sub-titled - at the nightclub where the music drowns out the dialogue and when characters speak backwards - but not in the British version. Apparently, director David Lynch changed his mind so often as to whether they should be included or not, by the time he came to a final decision, the British distributors had already made all their prints (without subtitles) and couldn't afford to make any more.
Originally announced for production shortly after the cancellation of Twin Peaks (1990), the film was shelved when several key members of the cast - notably Lara Flynn Boyle, Sherilyn Fenn and Kyle MacLachlan - declined to participate. MacLachlan, in particular, adamantly refused to appear for fear of typecasting. Director David Lynch managed to persuade the actor to return albeit in an abbreviated role, and created the character of Agent Chester Desmond (Chris Isaak) to compensate for Cooper's absence in the story. This created several continuity errors (the degree of which is still debated among fans) between the film, the series and several canonical tie-in novels.
Contrary to rumors that she refused the chance to reprise her Twin Peaks (1990) role (which is taken over by Moira Kelly) because of the film's nude scenes, Lara Flynn Boyle's absence from Fire Walk With Me was actually due to scheduling conflicts, as she had prior obligations to four other films.
Robert Engels claims the script that he and David Lynch wrote is much longer than the version that Lynch actually filmed. He claims there is enough story for a sequel. Indeed, as with many other Lynch films, about five hours of footage was shot. Many of the scenes that ended up on the cutting room floor involved characters who appeared in Twin Peaks (1990) but not in the movie. These scenes include:
Sheriff Harry Truman singing to Josie Packard
Johnny Horne's birthday party
Bobby Briggs' parents reading from the Bible
Doc Hayward performing magic tricks
a fight scene between FBI Agent Chester Desmond and Sheriff Cable.
The zigzag pattern on the floor of the Black Lodge is similar to the pattern on the floor of the lobby of Henry's house in Eraserhead (1977), also directed by David Lynch. The Black Lodge version of the pattern is much larger.
The convenience store sequence refers back to one of the first episodes of Twin Peaks (1990), when Philip Gerard, under the influence of Mike, tells Cooper that the Black Lodge spirits lived above a convenience store when in the human world. According to Michael J. Anderson (Man From Another Place) the scene originally ran for twenty minutes; only about one minute actually appears in the film.
The trivia items below may give away important plot points.
One pivotal scene deleted from the final film revealed the fate of Annie Blackburn (Heather Graham) after the ending of Twin Peaks: Episode #2.22 (1991). After escaping the Black Lodge, Anne was taken to the hospital where it was discovered that she was wearing the Owl Ring that belonged to Theresa Banks and Laura Palmer. A nurse then took the ring, and started laughing maniacally.
The movie originally ended showing Dale sitting in the Black Lodge, comforting Laura after she entered. It then cut to the last scene of the TV series - Twin Peaks: Episode #2.22 (1991) - with Harry breaking down the door of the bathroom and finding Dale smashing his head into the mirror and laughing. Dale tries to act like nothing happened, but is dragged off to bed. This was to confirm that it was Dale's doppelganger that escaped the Black Lodge.
Another deleted scene which took place after Laura's death extended the dialogue between Cooper and The Man From Another Place. Just after the dwarf says "I am the arm," Cooper notices that the ring disappeared. He then informs Cooper that someone else has taken the ring, and implies that Cooper is trapped in the Lodge forever.