Yep what I stated has been confirmed ( can't take credit another poster called this months ago), Ridley got his arm twisted.
*HUGE SPOILER WARNING*
http://collider.com/alien-covenant-original-story-prometheus-2/#david
Alien: Covenant is now finally in theaters, to a somewhat divisive response, but the film that
Ridley Scott ended up making wasn’t always the one he intended as the follow-up film to
Prometheus. Indeed, that (also divisive) 2012 movie was the
Blade Runner filmmaker’s highly anticipated return to the sci-fi genre, and he did so under the guise of a prequel to the film that first put him on the map:
Alien.
Passengers scribe
Jon Spaihts originated the
Prometheus script as a film that brought back the facehuggers and the iconic xenomorph, but when
Damon Lindelof was asked to weigh in, he shaped the script into more of a separate sci-fi film than a direct prequel to
Alien. Instead of focusing on that iconic monster, the film introduced precursors to the xenomorph while focusing more squarely on the Engineers, the beings that created humans in the first place.
The end of
Prometheus revealed that the Engineers had been using the planet that the Prometheus crash-landed on as a containment/creation zone for a biological weapon. They were headed to wipe out humanity when the organism they created turned on them, leaving behind the deadly tomb that the Prometheus crew finds. At the movie’s conclusion,
Noomi Rapace’s Dr. Elizabeth Shaw and
Michael Fassbender’s badly injured android David are the only two survivors, and instead of charting a course back to Earth, Shaw argues they should instead try to find where the Engineers came from to better understand why they wanted to snuff out their creation of humanity.
Shortly after
Prometheus’ release, both Scott and Lindelof were fairly open about their plans for a
Prometheus sequel,
with Lindelof revealing that the two had already plotted out the answers to questions posed in that film:
“Ridley was very interested in talking about, ‘What are the answers to the questions that
Prometheus is posing that are not necessarily definitively spelled out in the body of
Prometheus?’ I said to him, we should be prepared for people to feel frustrated if we’re going to be withholding, so we have to be very careful about what we’re saving for later because it’s not a foregone conclusion that there are going to be sequels, and so if there isn’t a sequel, just be comfortable with what we gave them in this movie.”
Lindelof continued, as the initial plan was for
Prometheus to spawn its own separate franchise further disconnected from
Alien:
“This movie has two children: One of these children grows up to be
Alien, but the other child is going to grow up, and God knows what happens to them. And that’s what the sequel to
Prometheus would be.”

Image via 20th Century Fox
Scott maintained that
it was pertinent to keep both Shaw and David alive at the end of
Prometheus to set them off on a path for the eventual sequel:
“I know where it’s going. I know that to keep [David] alive is essential and to keep [Elizabeth] alive is essential and to go where they came from, not where I came from, is essential.”
As for what Shaw and David would find upon meeting the Engineers,
Scott had already worked out that they would be portrayed as pretty evil beings:
“Because [the Engineers] are such aggressive fuckers … and who wouldn’t describe them that way, considering their brilliance in making dreadful devices and weapons that would make our chemical warfare look ridiculous? So I always had it in there that the God-like creature that you will see actually is not so nice, and is certainly not God. As she says, ‘This is not what I thought it was going to be, and I think we should get the Hell out of here or there won’t be any place to go back to.’
That’s not necessarily planted in the ground at the tail end of the third act, but I knew that’s kind of where we should go, because if we’ve opened up this door — which I hope we have because I certainly would like to do another one – I’d love to explore where the hell [Dr. Shaw] goes next and what does she do when she gets there, because if it is paradise, paradise can not be what you think it is. Paradise has a connotation of being extremely sinister and ominous.”

Image via 20th Century Fox
If you’ve seen
Alien: Covenant it’s at this point that you’re probably thinking, “Uh, what?” Indeed, the film that became the
Prometheus sequel doesn’t bear a ton of resemblance to the one that Scott and Lindelof were describing back in 2012, but that’s par for the course in Hollywood. Scripts get developed, evolve, and change, and clearly Scott opted to go a different direction with it.
Lindelof decided not to return to script the
Prometheus sequel, which is credited to
John Logan and
Dante Harper with a “story by” credit going to
Michael Green and
Jack Paglen. Obviously the biggest change here is the jettisoning of the Shaw character. While Rapace did return and shoot scenes for
Covenant, they ultimately landed on the cutting room floor and were released online as something of a prologue filling in the gap between what happened in
Prometheus and where we find David in
Covenant.
We see that Shaw painstakingly put David back together and then was put into hypersleep while David piloted the Engineer ship towards their home planet. That sequence ends with footage we
do see in
Alien: Covenant: David releasing the biological weapon on a legion of Engineers greeting the arrival of the presumed-lost ship.

Image via 20th Century Fox
As we learn in
Covenant, David developed an antagonistic relationship toward his own creator, Peter Weyland (
Guy Pearce) pretty much from the first minute he was “turned on.” But David played the waiting game, biding his time until he could exact revenge on his creator and his entire race—
and the progenitor of that species itself. Basically, David hates humanity so much, and finds it so inferior, that he develops a species of his own—a predatory killing machine that rips anything resembling a human to shreds.
So what happened to the story thread of following Shaw and David as they confront the Engineers? Well
Alien: Covenant basically puts the whole Engineer story to bed as David wipes out the entire species before the Covenant ship even lands (though it’s possible some colonies elsewhere still exist). In the context of the franchise, it appears we’ll never find out exactly why the Engineers targeted humanity for destruction—but Scott himself revealed the answer to that question back in 2012.

Image via 20th Century Fox
Essentially, in this initial story idea, we would discover that Jesus Christ was an Engineer emissary sent down to Earth to put a stop to brutal warfare.
He was crucified, the Engineers got mad, and humanity’s fate was sealed:
“We definitely did [have that in the script], and then we thought it was a little too on the nose. But if you look at it as an ‘our children are misbehaving down there’ scenario, there are moments where it looks like we’ve gone out of control, running around with armor and skirts, which of course would be the Roman Empire. And they were given a long run. A thousand years before their disintegration actually started to happen. And you can say, ‘Lets send down one more of our emissaries to see if he can stop it.’ Guess what? They crucified him.’”

Image via 20th Century Fox
I suppose it’s possible this story thread could still be explored in whatever the sequel to
Alien: Covenant turns out to be—Scott says he has one or two films left before we hit the timeline of the original
Alien—but the end of
Covenant seems far more concerned with David. Moreover, we’ve now answered that one big glaring question that an
Alien prequel posed: Who created the xenomorphs? It was your friendly neighborhood android David, who’s now in control of 2,000+ colonists aboard the Covenant as Daniels (
Katherine Waterston) and Tennessee (
Danny McBride) are in hypersleep.
Where things go from here is anyone’s guess, and even if Scott did come out and say exactly what the
Covenant sequel will entail, there’s no guarantee that story will stick as evidenced by his comments about
Prometheus 2 back in 2012. Scott says the script for the
Covenant sequel is already written, and it’ll be interesting to see if Daniels and/or Tennessee return, or if Scott once again unceremoniously kills off the protagonists of the prior film.
Whatever the case, it seems that Scott is now far more interested in telling David’s story than further exploring the Engineers.