Warning: Major SPOILERS for Alien: Covenant ahead
Alien: Covenant, Ridley Scott's latest in his ever-expanding sci-fi horror franchise, follows the crew of the sub-titular colonization vessel as they explore a presumed paradise only to discover the extra-terrestrial horrors that lie within. So far, so Alien. What makes the new movie stand out from the pack is how it takes many of the franchise's long-standing ideas - deceptive industrialism, sexual body horror, very bad robots - and marries it with the high-flying philosophy Scott has previously explored with Blade Runner and introduced to this franchise with Prometheus.
That aforementioned paradise is the former home of our creators, the Engineers, and after the first spate of killings in Covenant, the crew find themselves in the lair of the previous film's lone survivor, synthetic David, who has developed a deadly perfect organism - the series' iconic xenomorph - and secretly intends to wipe out the unsuspecting colonists as part of a much grander plan. The rest of the film is built on the unease over what he may or may not have done as they try to escape.
It's a big, far-reaching movie, and while there are definitely a lot of interesting elements within the basic story of the crew, for the most part they're accentuating the man at the center of all this, Michael Fassbender in the dual role as David and Walter. The robotic pair are the core of the movie's plot, themes and its show-stopping twist ending, and no doubt spell out the future of the series. As such, they should be the real focus of any analysis of Alien: Covenant's ending.
What Happened Between Prometheus and Alien: Covenant?
The Alien prequel timeline spans hundreds of thousands of years in its entirety and, as its opening shows Peter Weyland bringing David to life, Covenant itself manages to cover the better part of a century. As such, even only two movies in it's already a complex canon and warrants its own separate discussion. However, we do need to look at what happened in the ten years between Prometheus and Covenant to fully understand the latter's ending, specifically in regards to David.
In the original prequel, Michael Fassbender's android was on the surface a rigid automaton obeying orders from his creator, Peter Weyland, but displayed his own dark unique thoughts, treating humans as petri dishes - he incubates by proxy a proto-facehugger and Deacon - and at one point even hinting at contempt for his maker. Weyland was eventually battered to death by an Engineer using David's head (a creator killing his creation with its own creation) and David and Elizabeth Shaw left LV-223 in search of the Engineer homeworld.
On the journey, Shaw fixed up David and the pair formed an emotional bond. Once Elizabeth went into cryosleep for the long trip, David - now free with the death of Weyland - was left alone and began to learn about how the Engineers work. By the time he arrived on their planet, he'd decreed them a failure and instigated a mass extermination, dropping thousands of pods of the black goo pathogen over the central citadel and littering the planet with pods of black spores. Somehow his ship crashed and he began experimenting further with their tech to create a refined version. Once he'd exhausted his options there, David then turned his eye to getting off the planet, setting up Shaw's recognizably human Country Roads cover as a distress beacon.
This is alluded to in the movie itself and explicitly shown in the tie-in prequel Prologue: The Crossing, which you can watch in full below.
How Did David Make The Xenomorph?
The explicit purpose of the Alien prequel enterprise is to show where the xenomorph come from and, after vague allusions in Prometheus, we finally get an answer in Covenant: David bred them from the Engineer's biomechanical weapons.
In brief, the black liquid developed by the Engineers attaches itself to a living organism and rewrites their DNA, feeding on them and growing a creature before that violently escapes the host. David starts with the pods and spores created by his assault on the Engineers, which in its pure form with humans (it obviously alters different species differently) leads to the neomorph - a pale, spindly creature that emerges from two of the Covenant's landing crew upon first arrival.
When alone on the planet, David begins to probe the possibilities of the pathogen, experimenting on the surviving Engineers and Shaw. He endeavors to perfect the process, breeding the pods a la Mendelian inheritance until he reaches his perfect organism: the movie's protomorph, a nearly-finished xenomorph. He develops the eggs and facehugger, needing just a host to birth his creation - and he gets just that when the Covenant arrives, using Captain Oram as the protomorph's "mother."
- Alien: Covenant (2017) release date: May 19, 2017