Still confused by Alien: Covenant? Fret not, the home video release may offer some answers thanks to some incredibly revealing deleted scenes.
Covenant marketed itself on being a return to the franchise's space-horror roots, but it was very much a sequel to Ridley Scott's previous prequel Prometheus. We picked up with Michael Fassbender's Peter O'Toole-influenced android David, who, following the death of creator/father Peter Weyland, has evolved from dutiful, curious child into a life-developing psychopath of his own.
At the core of the film was the reveal that David bioengineered the iconic Xenomorph using the black goo pathogen favored by humanity's own creators the Engineers, with the film leaving him on the Covenant alone ready to enact his machinations on 2000 unsuspecting colonists
We did a series of articles explaining what exactly went down in the movie and what its ending meant upon release, but there were still gaps that required assumption leaps. Now, however, the Blu-ray's deleted scenes and related features provide a few more answers.
David's Xenomorph Experiments Explained
Covenant (and its prequel short film The Crossing) told of how David traveled from Prometheus' LV-223 to the Engineer homeworld with Elizabeth Shaw, whom he slowly developed feelings for after she repaired him following his premature beheading. Upon arrival at the planet, he exterminated the Engineers with canisters of black goo, believing them flawed Gods, and set about making his own prime species. He experimented on various beings, including Shaw, eventually synthesizing the eggs that hold the facehuggers that lay the xenomorph into a host.
Short film/epilogue Advent goes deeper into this inter-movie period. Although the actual alien biology is kept vague (being, you know, entirely made up) we get clarification of the liquid's DNA-altering capabilities, as well as how it affects various species differently. Importantly, we learn that it's a genetic nanotech, not organic; the Engineers made it and so its products are pre-existent, explaining how the xenomorph could appear in a mural in Prometheus.
The various stages of aliens are adaptations of this involving extensive meddling with indigenous life - we have confirmation that the species David's made in the film are the fourth generation of his meddling and it's suggested the facehugger is a mutation of a native creature on the planet. Overall, it appears David is playing with God's toys, rather than making his own playthings straight up. There's also written mention of "hive like mind", which makes the xenomorph's sound more bug like and ties more into Aliens, which we'd previously theorized was no longer canon.
The most interesting part in here, however, are more details on what he did to Elizabeth Shaw. Previously we knew David killed her as part of his experiments, but now the true horror of his designs comes to light. The Engineers were unsuitable subjects for tampering (likely due to his biological genocide), whereas human DNA was ripe for manipulation (perhaps because it first synthesized us) so David was forced to turn to Shaw. He wanted to make her "more than human" but when she made her (totally rational) reluctance clear he simply killed her and began to advance towards the zenomorph. All of this is delivered in the android's typically cold manner, making it all the more unnerving.
Covenant itself was rather light on Noomi Rapace, likely to avoid direct narrative connections to Prometheus, but the marketing has finally given her arc a sense of closure.
David's Plan Wasn't To Leave The Planet
A deleted scene also reveals a small yet key aspect to David's plan in the movie. His goal at the time seemed to be getting off the planet - hence using John Denver - but now it appears to be something a little more complex.
When he first leads the survivors across the barren expanse of the Engineer city, a cut sequence took them by a landing hole with several juggernaut space crafts in. This directly challenges the idea of David as Robinson Crusoe and instead makes the tale of him being stranded all an act. What he really wanted and was waiting a potential eternity for was humans on which to continue his experiments - at first just to birth his xenomorph. It seems that it was only learning of the colonists that tipped him to leave the lost paradise.
Now, though, he has a new plan teased at the end of Covenant, and the bonus features provide some context for that too.