1997 sequel Alien: Resurrection was one of Joss Whedon's first feature film scripts, but The Avengers director ended up none too happy with the finished product. While his work shaping the first two phases of the Marvel Cinematic Universe helped him graduate to full-on Hollywood power player, it can be easy to forget that prior to working with Marvel Studios, Whedon was seen more as a cult figure that appealed to hardcore genre fans with TV shows like Buffy the Vampire Slayer, Angel, and Firefly.
None of the films Whedon penned prior to The Avengers were big hits, aside from Toy Story, of which he was one of multiple credited writers. Back when Alien: Resurrection was in the works, Whedon was still very much someone trying to establish himself in the rough and tumble world of film and TV. The Buffy movie underperformed, and the follow-up TV series hadn't debuted yet. Writing a new entry in a successful sci-fi/horror franchise probably seemed like a great opportunity at the time.
Unfortunately, Alien: Resurrection proved to be a critical and commercial flop, killing plans for a fifth film in the franchise. Many would today hold up Resurrection as the worst entry in the Alien series, outside of maybe the Alien vs Predator films. Whedon is very much one of those people, having made his displeasure with the sequel clear on multiple occasions over the years.
Joss Whedon Is Upset About Alien: Resurrection
Even in interviews conducted after his success with The Avengers, Joss Whedon still clearly isn't over the pain of how Alien: Resurrection turned out. For one, the script Whedon wrote, as often happens in Hollywood, ended up bearing little resemblance to the final product. Since Whedon is the sole credited writer though, he tends to get all the blame for how bad the sequel turned out, which bothers him to no end. As Whedon said in one 2005 interview with In Focus magazine, "I don’t remember writing, “A withered, granny-lookin’ Pumkinhead-kinda-thing makes out with Ripley.” Pretty sure that stage direction never existed in any of my drafts."
Furthermore, in a 2013 interview with Total Film magazine, Whedon lamented how much he hates being associated with a "s**tty" Alien sequel, and how the internet ensures that'll now and forever be the case. He also thinks director Jean-Pierre Jeunet sabotaged Alien: Resurrection right off the bat by casting various roles poorly. He doesn't necessarily think the actors selected were bad, he just doesn't think they were right for their particular roles. While it's been a few years since Whedon has publicly discussed Alien: Resurrection, it's hard to imagine his feelings have mellowed much since, if at all.