According to director
Karyn Kusama, after finishing the movie, the studio fired her, re-cut the movie to a 71-minute long version that tested poorly and then asked her to edit the film again, but not back to her original vision. Huge parts of the plot were left out and even one character's sexuality of being gay was cut out by the studio.
It's possible that this 71-minute version of the film was an R-rated version which some producers wanted. Despite Kusama's objections, alternate scenes were filmed which for example showed more bloodier fights and bullet hits, and more nudity from Charlize Theron in several of her scenes. In the end, they decided to go with PG-13 rating so violence and nude scenes were cut, including an entire sex scene, although you can still see several quick shots of Theron's breasts in post-sex scene.
Kusama's original cut was about 30 minutes longer and it also had different score, composed by Johnny Klimek and Reinhold Heil, which was rejected by the producers and replaced with Graeme Revell's score while they were re-editing different versions of the film for test screenings. Trailers for the film show some of alternate scenes which could be from Kusama's director's cut, like Æon in different clothes after she wakes up.
