As Alien 3 concluded, we saw Lt. Ellen Ripley destroy the xenomorph creature on Fury 161, and confront Weyland Yutani face to face as they tried to attain the one last specimen- an alien queen - growing inside of her.
Rather than letting this happen, Ripley made the ultimate sacrifice by falling into the prison's giant furnace, ending her life and all possibilities for the xenomorph queen to propogate. It seemed to be a pretty definitive ending for the character, and for all intents and purposes, the final chapter of the Alien Trilogy had been written. There was, however, interest in continuing the series even though Sigourney Weaver was done with the Ripley character. Jorge Saralegui, 20th Century Fox's executive vice-president of production at the time, had a strong desire to move forward with Alien 4.
His concept was for Rebecca Jorden AKA Newt, to return to the series leading the way for a sort of, Alien: The Generation angle. Saralegui sought the aid of Joss Whedon, with whom he had previously worked on the film Buffy the Vampire slayer, believing the writer's style to be perfect for this new story. Amy Pascale's 2014 book, Joss Whedon: Geek King of the Universe, outlines this brief, shining moment in time where Newt was meant to lead Alien 4:
"Weaver had wanted Ripley killed off and had very little interest in returning to the franchise, so Saralegui decided to bring back Newt, the little girl Ripley saved, instead. Although Newt died at the beginning of Alien 3, Saralegui's idea was that she would be cloned because of the survival skills she demonstrated in Aliens, and would be used by Ripley's former employer to track down the alien for their own research. The cloned Newt, in effect, would become a Buffy-like character- a young girl imbued with special skills and strengths to take out a particular enemy. 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 just 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 favorite franchise that had gone astray. 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."
While earlier drafts of Whedon's Alien Resurrection screenplay have found their way online and made available for viewing, this 30-page treatment involvement Newt has not. We can only really speculate as to how this story was presented, and how closely it may relate to the final film released in 1997. Surely the general concept is there, of a military vessel and a cloning operation gone awry. Likely the supporting cast of the space pirates were there in some form.
By extension, the original ending concieved by Whedon, a showdown between our heroine and the newborn in a snowy forest on Earth. A climax on Earth always seemed to be something Whedon was particularly proud of, and especially disappointed with in how this was completely axed from the final film. Had this been a story starring Newt, instead of Ripley, such an ending would have been a good bridge into new possibilities of continuing the series. This would have acted more as a "Part One" in the Next Generation concept, instead of a "Part Four" in the Alien series. With either Ripley or Newt as the lead, the crucial factor is somehow being able to bring a character back from the dead. The conciet of Alien 4 has always been the cloning operation.
Either way, both the bodies of Ripley AND Newt ended up in the furnace, and the brief explaination from Dr. Gedimen is that tissue samples were found on Fury 16. The novelization of the film, written by AC Cripsin, offers some elaboration.
Here's an excerpt: "It was unprecedented work. The samples were varied enough, and there were plenty of cells, but the DNA was in chaos. It had been an amazing discovery to find that the embryonic Alien that had already infected Ripley’s body when the blood and tissues were taken had not stopped its invasion there. Like a virus, the embryo had actually invaded the host’s living cells—every last one of them—and forced them to change to accommodate its growth and development. It was a major breakthrough in adaptive evolution. It was a way to guarantee that any host, any host at all, would provide whatever it was the developing embryo needed, even when the host’s own body was inadequate. The infusion of Alien DNA into Ripley’s own had been how they’d managed to incubate her and her embryo. But it hadn’t been easy. They’d had to separate out the DNA right down to the RNA, reconstruct it, try to get it functioning… It had been work, incredibly hard and frustrating work, and it had taken years."
Essentially, this DNA snapshot was taken, at the exact moment Ripley lived with the alien queen in her chest, and it was retrieved by the Auriga's scientists. The suggestion in Pascale's Whedon biography is that Newt would have been cloned simply for her knowledge and experience with the xenomorph, rather than being host for a specimen. Assuming this wouldn't be a comics-inspired trip to the Alien Homeworld, then we can assume the Aliens would have also been cloned at some point by samples left behind. Again, not the most implausible thing the world: the quadraped alien on Fury left behind shed skin, plenty of drool and slime, and tiny pieces of itself after it was dosed in the cold water and exploded. This would end up drawing even further inspiration from the unproduced William Gibson concept of Alien 3, where samples left behind on the Sulaco and on the Bishop android were cloned, resulting in more aliens running amok.
But maybe, just maybe, they could have returned to a concept we saw only in the 1992 comic book adaptation of Alien 3. There, it is depicted that Newt was initially the host for the alien queen. It grew inside her, but when the EEV crashlanded into the waters of Fury, Newt began to drown. As an act of self-preservation, the queen embryo, not yet fully formed as necessary, escaped from Newt's throat, and found refuge in Ripley, where it remained until the end of the story. So, since Newt was, in fact, a host, this same DNA snapshot concept could have been applied to her clone as well.
No matter how we would have been able to get there, the idea remains the same. It's Newt as the main character in the new movie.
She's carrying the torch.
She's fighting aliens.
Looking at Newt as a character, and what was explored with her in the comics, there's a lot of trauma to be dealt with in the aftermath of Aliens. Memories of her family and her parents' doomed expedition to the alien derelict. The weeks of hiding and evading pursuit from the monsters that had overtaken the Hadley's Hope colony. And the daring escape that took place once Ripley and the marines arrived. it all would have left some deep psychological scarring. There could have been a lot to consider with shaping this character for another movie as she grew older. Joss Whedon did have plans, seemingly from the very beginning of his concept, to follow up with a fifth film that would have taken place mainly on Earth. Obviously, since Sigourney Weaver did end up reprising her role for Resurrection, the fifth film would have included Ripley 8 as well. But if things had turned out differently and the trajectory had played out as a new trilogy starring Newt, then it may have turned out similar to the original comics and the Earth War storyline.
But in finding ourselves back into the world of comics, I really think this 30-Page, Newt-starring treatment should see the light of day in some form. Given the history of seeing William Gibson's Alien 3 adapted into a comic, and Dan O'Bannon's original Alien screenplay adapted into a comic, why not give us a taste of the Alternate Alien 4?
The only problem is, those afformentioned comics were produced during Dark Horse's run, and the Alien property is now owned by Marvel. I'm not 100% sure if they'd even be interested in that, unfortunately.