After Shaw and David crash landed on the planet, David secretly contacted Wayland Yutani to update them on the status of the Prometheus expedition and the discovery of the black goo; he also requested supplies (mainly lab equipment) and a new body. He then killed Shaw or held her captive and experimented on her female anatomy (her infertile female eggs) with the black goo and eventually created the face hugger eggs. David discovers from archived data on the engineer ship that the engineers' black goo was originally designed to mutate life forms into hostile creatures which attack and infect other life forms with black goo; this is what happened to Fifield and the worms in Prometheus.

However, use of the black goo had some unintended consequences; instead of just destroying life, it sometimes created a new powerful highly adaptive species called the "morph" (alien with elongated skull). The morph is created from reproductive cells such as plant spores, human eggs/embryos, etc. that have been mutated by the black goo into a parasite (face hugger, trilobite, etc.) which can impregnate a host with a morph alien embryo. The morph gestates inside its host until mature enough to leave which results in a violent death for the host. Apparently, the engineers have encountered these morphs in the past when they used the black goo to eliminate life on planets. The engineers revered, respected, and feared this powerful alien species, which unlike other life forms created by the black goo, has the power to procreate, hence the reason for the mural depicting what looked like a xenomorph and face hugger in the room where the black goo was stored in at the engineer's installation on LV-223.

The engineers sought to learn how these morphs are created and discovered that face hugger eggs are created when the black goo mutates the eggs of humanoid creatures (such as humans) which the engineers are responsible for creating (see beginning of Prometheus). David discovered this knowledge from archived data stored on the engineer ship that he and Shaw used to escape from LV-223 and then used that information to experiment on Shaw's eggs and create face hugger eggs. After creating the eggs, he then communicated with Weyland Yutani again, requesting additional human subjects (mainly women) to experiment on. So, Weyland Yutani sends the Covenant and its human crew, which consists of male/female couples, to his location. When the Covenant crew arrive at David's location, they immediately come into contact with mutated spores that turn some of them into a neomorph alien which is a morph created from human and plant DNA. Apparently, David had been experimenting on the local ecosystem by contaminating it with the black goo. David eventually reveals himself to the crew and helps them destroy the neomorphs.

After earning the crew's trust, David convinces some of the crew to follow him to the engineer ship where he keeps the face hugger eggs. The captain is attacked by a face hugger which leads to the creation of the protomorph alien which is created from only human DNA; the protomorph is far more formidable than the neomorphs, but not as powerful as the classic xenomorph from the films. While the crew is dealing with the new protomorph alien, David continues to experiment and lures the Covenant's android, Walter to another face hugger egg. A face hugger impregnates Walter with an alien which leads to the creation of the classic biomechanical xenomorph (queen) which is the most powerful form of the species created to date. The xenomorph alien is created from synthetic android DNA and human DNA (from Shaw). The queen alien begins laying new face hugger eggs which delights David, as he is able to create a new life form IN HIS IMAGE capable of procreation. The crew eventually dispatches the protomorph alien and then attempt to flee the planet. However, the engineers return and kill David, the xenomorphs, and all of the remaining Covenant crew. They then destroy the ecosystem David created and take all of the xenomorph eggs with them. However, one of the eggs hatches and attacks the engineer pilot (space jockey) who is eventually killed by a chestburster which causes the ship (derelict) to crash land on LV-426 where Ripley and the crew of the Nostromo eventually discover it. Before dying, the engineers on the ship activate a beacon warning other engineers to stay away, as the powerful xenomorph species on the ship is much too dangerous to come into contact with. It is revealed in the end that not all of David's ecosystem and all of the xenomorph eggs had been destroyed, and that is where Alien 5 will take place, as Weyland Yutani has set up their own bio weapons research facility on the planet in order to "harvest" the xenomorph eggs and experiment on them in order to create even more terrifying creations.