Warning: This list contains spoilers for the entire Alien franchise.
Ever since the first chestburster exploded out of Kane and onto the big screen, fans of the Alien franchise have tried desperately to work out the mysteries of Xenomorph mythology. The six features in the Alien saga (eight if you include the less-than-stellar Alien vs. Predator films) have each expanded the lore in new and unexpected ways. Even with 40 years' worth of films to draw from, a lot of nagging questions about the franchise remain. Why did the Engineers create the Xenomorphs? Why is Ripley so important? And what's with David's flute fascination?
We may never learn the answers to these questions, but that hasn't stopped the internet from trying. Dozens of fan theories exist on the web that aim to tie the films together in a more cohesive way. Many are completely ridiculous, but others genuinely make the films better. Only you can choose which fan theories are essential to the franchise - and which should be thrown out the airlock for good.
In Alien: Covenant, there's a scene where David travels to an unknown world and releases death upon the entire population. The aliens look like Engineers, but their clothes and technology seem far less sophisticated than anything we've previously seen.
Redditor /u/reece1495 suggests these are not Engineers, but another race they created in their own image. Unlike humanity, this race is much more peaceful, which is why the Engineers built a docking station on their planet. They viewed this experiment as a success and planned to visit them again, which is why the crowd forms and celebrates David's arrival.
In the very beginning of Prometheus, we see an Engineer give his own life to provide the organic building blocks for an entire planet. This stuck with one former Redditor, who penned a theory suggesting the Engineers believe death is essential to the creation of life. So when Peter Weyland shows up with his android, it's an affront to everything the Engineers represent.
Weyland has not suffered for his creation. In fact, he's using his creation in a selfish attempt to gain immortality. That's why the Engineer becomes enraged and goes on a murderous rampage.
In Alien, Ripley discovers that Weyland-Yutani was aware of the Xenomorph presence and sent the Nostromo to bring the creature back to Earth. But how did the company know about the Xenomorphs, and why were they so eager to bring them to Earth?
Redditor /u/starwarsunderpants believes the android David was secretly pulling the strings all along. The theory suggests that after the events of Prometheus and the death of Peter Weyland, David somehow took control of the company from deep space. David's directions then led Weyland-Yutani to the Xenomorph, and he dubbed the crew of the Nostromo expendable. It makes sense given his obsession with the aliens in Prometheus and his distaste for humans.
In Alien: Covenant, David manages to "create" the first Xenomorph by experimenting with the Neomorphs created by the Engineers. His pursuit is all for naught, though, seeing as the Xenomorph eggs in the original Alien were in stasis for thousands of years.
This theory by Redditor /u/megatom0 suggests that David didn't really create the Xenomorphs audiences are familiar with; instead, he reverse-engineered the Engineer's artificial bioweapons. Basically, the Engineers found the Xenomorph species and genetically altered them to make their own personal weapons. This is why the Xenomorphs in Covenant and Prometheus look different - they were created as tools of destruction.
David inadvertently creates a specimen more similar to the original Xenomorphs, which is much more hostile and mindless than the Engineers' creations.