Executive Meddling: The reason the theatrical cut was so much shorter than the Director's Cut. Fox wanted a Gladiator style action movie with a romance subplot, rather than the political drama Scott and co created. On top of that, they thought audiences wouldn't be able to handle a 3 hour film, disregarding high grossing films like Titanic and The Lord of the Rings. The theater-released version was panned, yet the Director's Cut was critically acclaimed as one of the best movies of the year.
Ridley Scott wanted the character of Sibylla to become a nun at the end of the film but the studio insisted it end with her and Balian ending up together.