Butterfly Baby: the film's deleted epilogue was shot four different ways (all of which can be seen on the DVD and Blu-Ray releases of the film).
In the version of the scene that was originally scripted (and previewed for the Los Angeles test audience), Veronica Quaife is seen in bed with Stathis Borans (having married him) some time after Seth Brundle's death.
She awakens from another nightmare in which she gives birth to Brundle's child, and Stathis reassures her that she is safe, and that the baby she is now carrying (having presumably aborted Brundle's) is his.
Veronica then falls back to sleep, and she is now dreaming of a beautiful human baby with butterfly wings hatching from a cocoon and flying off towards a distant light source.
The other filmed versions of the epilogue:
Veronica in bed with Stathis (much the same as the version that was previewed), but without her being pregnant. Instead, Stathis reassures her that "there's no baby". She then falls back to sleep and has the butterfly-baby dream.
Veronica waking up alone and in her own bed, then falling back asleep and having the butterfly-baby dream. In this version, she is clearly still pregnant with Brundle's baby.
Veronica waking up alone and in her own bed, then having the butterfly-baby dream. In this version, she is not visibly pregnant (thus leaving the ending ambiguous).
The epilogue was intended as an upbeat bookend for Veronica's earlier maggot-baby dream, and to give the surviving characters a more hopeful ending.
However, the coda did not fare well with the preview audience, since they were too stunned by the film's climax to focus on the coda, which raised a number of questions.
Further, due to the dynamics between the characters that evolved during filming, the chemistry between Brundle and Ronnie proved so strong that no one wanted to see her end up with Stathis Borans (which is one reason why the alternate, Borans-less versions of the coda were shot).
The filmmakers also agreed that the story should end with Brundle's mercy-killing at Veronica's hands, despite the unanswered questions about Veronica's unborn child that would be raised by the deletion of the epilogue.
The climax of the film also went through several incarnations in the various drafts of the script before the final version was filmed:
In one early version of the ending, Veronica is unconscious after Brundlefly throws her into Telepod 1.
When the Brundlething emerges from the prototype Telepod, the raging and mortally wounded creature crawls toward the injured Stathis Borans, who manages to grab a loose wire jutting from the Telepod/human/fly-hybrid creature's back and jams it into an electrical socket. The Brundlething is liquified by the electricity.
A later version of the scene is nearly identical, except that the Brundlething crawls toward Stathis (whether it wants to attack him or is just desperate for help is left ambiguous) and then dies.
In the version of the script that appears on the 2005 DVD, Veronica is conscious during the final scene, and when the Brundlething emerges from the receiving Telepod and crawls toward her, she aims Stathis' shotgun at it, but the creature ends up dying at her feet.
Eventually, this was slightly changed to the mercy-killing seen in the completed film.
The Academy Award-winning makeup was designed and executed by Chris Walas, Inc. over a period of three months. The final "Brundlefly" creature was designed first, and then the various steps needed to carry protagonist Seth Brundle to that final incarnation were designed afterwards.
The transformation was intended to be a metaphor for the aging process. To that end, Brundle loses hair, teeth and fingernails, with his skin becoming more and more discolored and lumpy.
The intention of the filmmakers was to give Brundle a bruised and cancerous look that gets progressively worse as the character's altered genome slowly asserts itself, with the final Brundlefly hybrid creature literally bursting out of Brundle's hideously-deteriorated human skin.
The creature itself was designed to appear horribly asymmetrical and deformed, and not at all a viable or robust organism. Various looks were tested for the makeup effects. Some early test footage can be seen on the 2005 The Fly: Collector's Edition DVD, as well as the Blu-ray release.
The transformation was broken up into seven distinct stages, with Jeff Goldblum spending many hours in the makeup chair for Brundle's later incarnations.
STAGES 1-2: Subtle, rash-like skin discoloration that leads to facial lesions and sores, with tiny fly hairs dotting Goldblum's face, in addition to the patch of fly hairs growing out of the wound on Brundle's back.
STAGES 3 and 4-A: Piecemeal prosthetics covering Goldblum's face (and later his arms, feet, and torso), wigs with bald spots and crooked, prosthetic teeth (beginning with Stage 4-A).
STAGE 4-B: Deleted from the film, this variant of Stage 4 was seen only in the "monkey-cat" scene, and required Goldblum to wear the first of two full-body foam latex suits.
STAGE 5: The second full-body suit, with more exaggerated deformities, and which also required Goldblum to wear distorting contact lenses that made one eye look larger than the other.
STAGE 6: The final "Brundlefly" creature (referred to as the "Space Bug" by the film's crew), depicted by various partial and full-body cable- and rod-controlled puppets.
STAGE 7: Another puppet which represented the mortally-injured Brundlefly/Telepod fusion creature (initially dubbed the "Brundlebooth" and later the "Brundlething" by the crew) as seen in the film's final moments.