In the commentary on the "Director's cut" DVD it is mentioned that an alternate ending was filmed where Dennis Farina's character lives. It was later changed after they decided he would have been a witness to everything and it would not have worked. Also several scenes were mentioned to be changed or heavily cut. One of them being a big reshoot right as Ben Affleck is going back to his hotel room after he finds out about Monster and Ashley not being brother and sister.
The director's cut features around 20 minutes of extra and re-edited footage. Included are new and extended scenes between Rudy and Ashley discussing their situation when kidnapped by Gabriel. Also included is an extended and more graphic version of the scene where Gabriel throws darts as Rudy, also a scene where he heals his wounds from the darts is included as well as an extended love scene. Other changes include the omission of "Love Rollercoaster" from the casino scene, which is replaced by a longer version with a much more suspense twist to it. Finally, another scene is extended where Gabriel shoots the ice around a fisherman sending him into the freezing lake to die as opposed to the original version which merely hinted at his killing the man.