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Impressed with his work as a screenwriter, 20th Century Fox hired Joss Whedon to write the film's script. Whedon's initial screenplay had a third act on Earth, with a final battle for Earth itself.cite-ref-gits09-8-0[7] Whedon wrote five versions of the final act, none of which ended up in the film.cite-ref-gits09-8-1[7]

The studio initially imagined that the film would center around a clone of the character Newt from Aliens, as the Ellen Ripley character had died at the end of Alien 3. Whedon composed a thirty-page treatment surrounding this idea before being informed that the studio, though impressed with his script, now intended to base the story on a clone of Ripley, whom they saw as the anchor of the series.cite-ref-9[8] Whedon had to rewrite the script in a way that would bring back the Ripley character, a task he found difficult. The idea of cloning was suggested by producers David Giler and Walter Hill, who opposed the production of Alien Resurrection, as they thought it would ruin the franchise.cite-ref-from-the-ashes-10-0[9]

Sigourney Weaver, who had played Ripley throughout the series, wanted to liberate the character in Alien 3 as she did not want Ripley to become "a figure of fun" who would continuously "wake up with monsters running around". The possibility of an Alien vs. Predator film was another reason for the character's death, as she thought the concept "sounded awful". However, Weaver was impressed with Whedon's script. She thought that the error during Ripley's cloning process would allow her to further explore the character, since Ripley becoming part-human and part-Alien would create uncertainty about where her loyalties lay. This was an interesting concept to Weaver, who thought the film brought back the spirit of Alien and Aliens.cite-ref-from-the-ashes-10-1[9] Weaver received a co-producer credit and was reportedly paid $11 million.cite-ref-beauties-and-the-beast-7-1[6]

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