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The film had originally been scripted with the Betty arriving on Earth, landing in the ruins of Paris, with Ripley and Call sitting down and trying to decide what they are going to do. Ripley says she doesn't know what to do, because she is a stranger to Earth. The scene was storyboarded and filmed, but never finished in post-production. Instead, it was re-written as Ripley and Call looking at Earth from above, aboard the Betty. It wasn't until 7 years later that director Jean-Pierre Jeunet was approached to make a special edition of his movie. Although he was quite happy with the old version, he remembered the originally scripted ending and agreed to finish the old scene.
Sigourney Weaver originally refused to do a fourth Alien film. When asked why she changed her mind, she replied, "They basically drove a dumptruck full of money to my house".
Sigourney Weaver made the behind-the-back half-court basketball shot successfully after 3 weeks of basketball practice, tutored by a basketball coach. Her conversion rate during this time was 1 of over 6 shots, but the distance was much lower than it would be in the actual scene. When the day came to shoot the scene, director Jean-Pierre Jeunet wanted to have the ball dropped in from above, rather than wait for Weaver to sink the shot herself, which "would probably take about 200 takes." Weaver insisted she could get the shot in herself, and was allowed to do. Though it is commonly said that she sank the basket on her first attempt, it actually took her endless takes to complete the stunt. Jean-Pierre Juenet gave her one last try to sink the basket before they would give up and use CGI or a second ball. The very next take, Sigourney Weaver successfully managed the trick. Ron Perlman broke character and began smiling when he saw it, and people on the set started cheering. The editors looked at the shot, and decided there was "enough room to get the scissors in." Weaver was excited about making the shot, but Jeunet was concerned audiences would believe the shot to be faked due to the ball leaving the frame. Upon Weaver's insistence, he kept the shot as it was. Weaver described the miracle shot as "one of the best moments in her life", after her wedding day, and the birth of her daughter.
Jean-Pierre Jeunet wanted to have a scene where a mosquito bites Ripley, then vanishes into smoke because of her acid blood. Eventually, he dropped the idea after the SFX team told him how much it would cost.
The opening shot of Ripley cloned, albeit as a young girl, was based on photographs which Sigourney Weaver had given the special effects crew of herself as a child.
Actor Ron Perlman nearly drowned while filming the underwater sequence. At one point, when trying to surface, he hit his head on a sprinkler in the ceiling, knocking him out cold. He was rescued by nearby film crew members.