Whedon writes the Alien Resurrection script

leading from

Alien Resurrection
and 
Alien 3: The end of Ripley? 

a) Reaching Joss
The people at Fox said to Jorge Saralegui "Okay, why don't you start working on it and find a writer?"
Saralegui reached out to Joss, because the Buffy movie script demonstrated his ability to bring such a character to life.

Joss who was getting over his frustrations with the handling of his script in Waterworld and had also got married to his girlfriend Kai, was incredibly excited and agreed to take on the project.

This was the chance of a lifetime - an opportunity to right the path of a favourite franchise that had gone astray.

b) Deciding to write Alien Resurrection
When he was first asked to write the next Alien saga, Joss didn't hesitate.

Alien was for him a sacred text and he couldn't turn it down. Enthralled by Alien and Aliens, Whedon felt (as many did) that Alien 3 was a disappointment.

He didn't like the fact that they actually had a scene where people he didn't know were killed by the alien. To him it was all too much like Friday The 13th .

While he found it beautiful, he found it neither exciting nor scary, and so it was a travesty.

He wanted every scene to contain something that amazed him and wanted to do something comparable to Evil Dead where it's menacing and then about twenty minutes into it, the action starts and never stops.

However the studio were talking in terms of Alien Resurrection being a kind of a 'place holder'. They said "We want to do Earth or the big Alien planet, but we're not convinced yet that the franchise has legs. So we want a smaller story."

c) The Golden opportunity
It was as if he was being given a golden opportunity to change the future of the Alien franchise by writing a script that would put it on the path to glory once again.

Initially, 20th Century-Fox wasn't sure they could get Sigourney Weaver to play the role of Ripley again. So Joss was asked to write the script without Ripley who, after all, had died at the end of Alien 3.

He banged out a script without Ripley,  going with Saralegui's idea about resurrecting Newt from the dead as the main character and was pleased with the result.

d) The Studio executives' cold feet
A few months later, after reading their thirty-page film treatment, the studios executives panicked, they told Joss and Saralegui that they found the reboot idea exciting, but they were worried about the box-office success of an Alien film without Ripley. Then they made Sigourney a deal she couldn't refuse, and asked Joss to go back to the drawing board.

e) Rebelling at the drawing board
At first, Joss rebelled against the idea of scrapping their Newt concept to revive Ripley, thinking  "Bullshit, she's dead." which is precisely what Newt was after the beginning of Alien 3 although it appeared that he didn't seem to bother him.

Since he was also a longtime fan of the Alien series, and this was his chance to be involved, so he eventually went back to the drawing board.

With only the parameters of "Scary like Alien. Exciting like Aliens. Add in Ripley" to guide him. Joss found it much more difficult than his first go-round.

f) Basic plot of final story
Joss' s script for Alien: Resurrection takes place two hundred years after Alien 3. Scientists aboard a military spaceship have used a genetic sample from the prison planet to create a clone of Ellen Ripley, in the hopes of harvesting more aliens for study. 

Later, a ragtag crew of mercenaries arrives to deliver human bodies, which the scientists plan to use for the alien incubation. Call, an android with the group, recognizes Ripley and tries to kill her, suspecting the truth about the clone's purpose. 

Unfortunately, the queen has already been extracted and the breeding process is underway. 

When the captive aliens escape and kill most of the military personnel, the ship's emergency systems kick in, sending the vessel back to Earth. Ripley and the mercenaries struggle to find a way to destroy the ship before the aliens reach Earth.

 

g) Ripley's torturous resurrection
Joss knew if he was going to bring such a beloved iconic character back to life and have the audience accept it, he needed the resurrection to feel real, not just like a sci-fi metaphor. 

Joss had to create "a total identification" between the audience and the Ripley clone; he needed to acknowledge the difficulty viewers would have in accepting the character's rebirth by making it hard for the character herself to accept.  

The film was not just saying "We've brought her back, let's make the movie.", Joss wanted it to be the central issue of the movie that they brought her back, and once you do that, everything must be different.  

When somebody comes back from the dead, especially in a movie where death the ultimate threat, one can't just say "It's okay, anybody can die and come back."  

 It was very important for him that it should be very torturous, grotesque process so that people will viscerally feel what it's like to be horribly reborn in a laboratory, and then the whole question  of what she is , is raised. 

Is she human? 

Has she changed. 

There was the factor that she was pregnant with an alien. 

Is she all human or is there something wrong there? 

There would be a lot of issues

h) An Alien IV
His idea was that if he wrote the fifth movie and it had his writing credit on it, then it's going to be set on Earth and it's going to be very different from the last one.

He thought that another Alien movie would have to be pulled out of the tin can that the Alien Resurrection and Alien 3 had been stuck in, as he wanted to see something happening in the way that Cameron's film Aliens followed on from Alien was like an explosion and that had to be done again and meant going in a new direction


 Source quotes

1. After receiving the go-ahead from the studio to develop a treatment, Saralegui reached out to Joss, because the Buffy movie script demonstrated his ability to bring such a character to life. Joss was incredibly excited and agreed to take on the project. This was the chance of a lifetime - an opportunity to right the path of a favourite franchise that had gone astray. (Joss Whedon: Geek King of the Universe ")
2. When he was first asked to write the next Alien saga, Joss didn't hesitate. Alien was "sacred text" and Joss couldn't turn it down. Enthralled by Alien and Aliens, Whedon felt (as many did) that Alien 3 was a disappointment. "I think the fans were robbed in the third one. They actually had a scene where people we didn't know were killed by the alien. That's Jason, that's bullshit, because nothing is more boring than people you don't know being killed. [Alien 3] was beautiful but it was neither exciting nor scary, which is a travesty. I just want every scene to contain something amazing, I want to do Evil Dead where it's menacing and then about twenty minutes into it the action starts and never stops."( Joss Whedon The Genius Behind Buffy)
3. Joss was given a golden opportunity to change the future of the Alien franchise by writing a script that would put it on the path to glory once again. Initially, 20th Century-Fox wasn't sure they could get Sigourney Weaver to play the role of Ripley again. So Joss was asked to write the script without Ripley who, after all, had died at the end of Alien 3. He banged out a script without Ripley and was pleased with the result.( Joss Whedon The Genius Behind Buffy)
4. A few months later, the Studio panicked, worrying that they wouldn't be able to generate the box-office success they needed without Weaver. They made her a deal she couldn't refuse, an asked Joss to go back to the drawing board. Joss initially rebelled, thinking, 'bullshit, she's dead," but came around to thinking that reviving Ripley could be very powerful. But, much as he tried to do in season six of Buffy, Joss wanted to make her resurrection real, and not without a price.( Joss Whedon The Genius Behind Buffy)
5. After reading their thirty-page film treatment, studio executives told Joss and Saralegui that they found the reboot idea exciting, but they were worried about the success of an Alien film without Ripley. At first, Joss rebelled against the idea of scrapping their Newt concept to revive Ripley. But he was also a longtime fan of the Alien series, and this was his chance to be involved, so he eventually went back to the drawing board. With only the parameters of "Scary like Alien. Exciting like Aliens. Add in Ripley" to guide him. Joss found it much more difficult than his first go-round. (Joss Whedon: Geek King of the Universe ") 
6. Joss' s script for Alien: Resurrection takes place two hundred years after Alien 3. Scientists aboard a military spaceship have used a genetic sample from the prison planet to create a clone of Ellen Ripley, in the hopes of harvesting more aliens for study. Later, a ragtag crew of mercenaries arrives to deliver human bodies, which the scientists plan to use for the alien incubation. Call, an android with the group, recognizes Ripley and tries to kill her, suspecting the truth about the clone's purpose. Unfortunately, the queen has already been extracted and the breeding process is underway. When the captive aliens escape and kill most of the military personnel, the ship's emergency systems kick in, sending the vessel back to Earth. Ripley and the mercenaries struggle to find a way to destroy the ship before the aliens reach Earth. (Joss Whedon: Geek King of the Universe ") 
7. Joss knew if he was going to bring such a beloved iconic character back to life and have the audience accept it, he needed the resurrection to feel real, not just like a sci-fi metaphor. Joss had to create  'a total identification' between the audience and the Ripley clone; he needed to acknowledge the difficulty viewers would have in accepting the character's rebirth by making it hard for the character herself to accept. "It's very important to me that it's a very torturous, grotesque process so that people will viscerally feel what it's like to be horribly reborn in a lab," Joss said. ' Is she human? Has she changed? ... She was pregnant with an alien.... Is there a little something wrong there?" (Joss Whedon: Geek King of the Universe ") 
8. Joss Whedon: "We're not just saying, "We've brought her back, let's make the movie." It's the central issue of the movie, the fact that we bring her back. We know that once you do that, everything must be different. When somebody comes back from the dead, especially in a movie where death the ultimate threat, you can't just say "It's okay, anybody can die and come back. " It's very important to me that it's a very torturous, grotesque process so that people will viscerally feel what it's like to be horribly reborn in a lab. And then the whole question of what is she raised. Is she human? Has she changed? There is the factor that she was pregnant with an alien. Is she all woman? Is there a little something wrong there? There are a lot of issues. ( Joss Whedon The Genius Behind Buffy)
9. Joss was worried that Weaver would want to see a more likeable Ripley than the one he envisioned. To great relief on both sides, Weaver told Joss she loved his original script and how he made the concept of cloning very personal. She liked how Ripley, sharing both human and alien DNA, faces new questions about where her loyalties lie. She told him to push her character further and asked "What if I'm ever stranger? What if I have more Alien and less human in me?" (Joss Whedon: Geek King of the Universe ") 
10. 'She created an extraordinary character." Joss said. (Joss Whedon: Geek King of the Universe ") 
11. Joss Whedon: If I write this movie and it has my writing credit on it then it's going to be on Earth. And it's going to be very different from the last one. (SFX, Alien Speculation)  
12. Joss Whedon: The studio talked about Alien Resurrection as a kind of 'place holder'. They said " We want to do Earth or the big Alien planet, but we're not convinced yet that the franchise has legs. So we want a smaller story."  I don't think you can do that with Alien V. I think that the time of people running around in a tin can has passed. You have to work on a broader canvas otherwise it becomes an episode and not a new movie. The way Cameron exploded from the first to the second, you have to do that again, and that means going to somewhere anew. (SFX magazine, Alien Speculation)
13. Jorge Saralegui: It was a matter of convincing them [the studio] to give it a shot. At the time, Ripley had died and it was Sigourney's idea to kill her, so we had no intention of bringing her back, we didn't think she'd want to come back. We had the notion of having Newt cloned and it could be Alien: The Next Generation.  The people at Fox liked the idea enough to say "Okay, why don't you start working on it and find a writer? " The first person I thought of was Joss Whedon. This is after he wrote Buffy The Vampire Slayer - the movie script a, not the TV series. (Starburst)
14.  How Ripley was brought back
    a) GEDIMAN: How did we get you? Blood samples from Fiori 16. On ice. (Alien Resurrection script)

    b)  CALL: Christie, she's not human.  Wren cloned her because she was carrying an alien in her.  (Alien Resurrection script)