BIG TIME SPOILERS for Alien: Covenant follow. Come back after you've seen the film!
It's clear from the get go in Alien that the xenomorphs are more than just your typical alien life form. Their appearance and chest-bursting methods are entirely new to the crew of the Nostromo and you'd think a creature as unique as a xenomorph would at least have been documented at some point. No, there's clearly something else going on as Ripley and the crew discover the alien eggs in the Engineer ship on LV-426. The origin of the xenomorph has been a long unanswered question in the Alien franchise, but Ridley Scott finally got around to revealing the answer in Alien: Covenant.
Half Prometheus movie, half Alien movie, Alien: Covenant tries to have its cake and eat it too, pondering the ethics of creation and religion while a space monster kills people having shower sex. It's a complicated movie trying to do complicated things and while it gets respect for digging into these deep ruminations, most of the questions it raises stay up in the air. However, it does answer arguably the biggest question of the Alien franchise: where do xenomorph's come from? Well, it all has to do with a nut bag android named David.
Yep, David created the xenomorph as we know it today. First introduced in Prometheus, David (played by Michael Fassbender) is... well, he's a difficult character to sum up in a few words, so let's just say he's a guy operating on lots of conflicting emotional levels. David is an android created by Peter Weyland himself and his particular model can do more than serve; He can create. Creation is David's thing, as the android becomes obsessed with both his creators and the creators of his creators, the Engineers. Throughout Prometheus, David is the guiding hand of events that eventually kills everyone but himself and Dr. Elizabeth Shaw. The film ends with the two of them taking off in an Engineer ship, on course for the Engineer homeworld.
And find the homeworld they do, but it doesn't end pretty. David has something of a god complex. He thinks himself superior to the ones who created him and seems to deeply loathe all organic life. The Engineers developed a type of virus, a black goo that results in death to whoever comes into contact with it. David experiments with this pathogen and ultimately unleashes a horde of bombs on the Engineer planet, killing all organic life -- minus the plants.
David is now the sole resident of the planet and for several years is left to his own devices with knowledge from a highly sophisticated race of beings. The android likes to keep his hands busy and decides that he can do better than a god. Using his pathogen, he experiments with creating a new race of creatures, a "perfect life form" that lives up to the standards he's built for himself. His lair is covered with scrolls of drawings that strongly resemble the original art of H.R. Giger, the man who designed the original Alien. Strange mutated creations of varying sizes lay dissected on tables (David considers himself something of a zoologist). We see one stage of his work in the form of a neomorph, a white skinned creature that's the early cousin to the xenomorph.
Somehow, David manages to accomplish his goal of the perfect life form by creating a small group of eggs that should be instantly recognizable to Alien fans. However, he's missing one key ingredient to make his Frankenstein's monster a reality and ironically, it's the thing he eradicated himself: organic life. Luckily (for David), the unsuspecting crew of the colonist ship the Covenant arrives on his planet, giving him some 14 test subjects to work with. He lures Captain Oram (Billy Crudup) to where he keeps his "successes" and Oram becomes the first man to ever succumb to a face hugger. Soon after, a true xenomorph emerges from his body, David's perfect life form. It runs amuck in short order and the film eventually ends with David in possession of two alien embryos and an entire ship full of sleeping colonists at his disposal.
Of course, there are more lingering questions. The Covenant Xenomorph has a few differences from the one in the first Alien, so does David continue his tinkering or has his creature evolved on its own? Also, what about the Alien Queen or LV-426? We have to wait for those answers, but at the very least we know who is to blame for creating the perfect killing machine.