After the success of Alien and the massive success of Aliens, everybody wanted to do the next Alien sequel. Most early scripts had a recurring theme of Ripley (the star of the franchise) and Hicks (the military survivor from Aliens) teaming up and taking the fight to either the Alien homeworld or battling the creatures on Earth. Unfortunately, none of these scripts proved different or even suitable enough for filming.
Having already invested much money into the development and hiring of various Hollywood writers and directors, Fox eventually settled on Vincent Ward's bizarre idea of a wooden planet populated by religious monks who've turned their back on technology. Some time into the development of this idea, studio execs suddenly produced a list of changes, which angered Ward and forced him to leave.
This left the pre-production process in some what of a mess, with half built sets and a muddled script. Fox went on to hire David Fincher, who was willing to follow their changes made to Ward's story, making the wooden planet an old mining colony instead. The problem that everybody was now faced with was that Fox had already set a release date, and without a finished script, there was no choice but to begin production and make things up as they went along.
During the production process, Fincher was constantly being undermined by Fox, who would tell him to cut various parts of the film or simply not to shoot some scenes. In the end, Fincher walked out during post-production, which explains how the movie was released with the butchered theatrical cut and sub-standard special effects. Fox then invented a smokescreen to cover themselves of any wrong doing, instead placing the blame on Fincher. Even the featurettes of the Alien Quadrilogy release were cut down by Fox to cover themselves of any wrong doing.
The story of the film, then, is a surprising direction after Aliens. Many were expecting the previously mentioned battle with the aliens on their homeworld or Earth. Instead, Alien 3 dealt more with the character of Ripley than the alien. This storyline was difficult to embrace by the viewing public because of its dark atmosphere, where Ripley is once again on her own after the other survivors from Aliens (Hicks and Newt) are killed off-screen during the opening titles. Aliens director James Cameron called this "a slap in the face" to Aliens fans.
Similar problems included an inexplicable facehugger egg on the Sulaco at the beginning with no explanation as to how it got there, nor any way it could fit with events seen at the end of Aliens. Due to cuts made by Fox, several sub-plots involving religious prayer and a disturbed prisoner named Golic were removed, when they were actually important to the storyline. This left the theatrical release with a number of plot holes and some disappointing post-production effects.
When the Quadrilogy set was released, a new restored version of Alien 3 was seen for the first time, solving many of the plot problems above, though obviously not un-doing the deaths of Hicks or Newt nor explaining the presence of the egg. Still, this new version, which is the version included in this definitive edition, is so much better than the theatrical version. Unfortunatley, while better, Alien 3 is still not the classic that Alien or Aliens were. Maybe if Fincher had been allowed to properly finish the film, it may have fared better.