The Alien franchise is one of the most famous collections of films in the science fiction genre. Beginning with Alien in 1979, it redefined our cinematic concepts of space exploration. Not only did it paint a gritty and vivid near-future for those who had grown up on jumpsuits, jet-packs, and ray-guns, it also presented probing psychological questions that preyed on some of humanity's greatest anxieties about discovering it's not alone in the universe.
There have been a total of six films in the Alien franchise, eight if you count both Alien vs Predator movies). Ever since Ridley Scott decided to answer the question "Where did the aliens come from?" in Prometheus and Alien: Covenant, the questions have only increased, leaving it up to the fans to theorize the logic of the films. Here are 5 things that don't make sense and 5 fan theories that do in the Alien franchise.
MAKES NO SENSE: DIFFERENT ALIEN GESTATION PERIODS
The Alien vs Predator franchise convoluted many aspects of both sci-fi properties. In particular, one of the aspects it mired was the period of time it takes for a Chestburster to gestate inside a host before killing them. In these films it only took a matter of hours, resulting in a complete infestation of xenomorphs to a known human settlement in less than a day.
As we know from the colony in Aliens, this would have taken weeks. By the time that Prometheus, the xenomorph origin film came out, a relative of the Facehugger (the Trilobite) grew rapidly in a human womb and even more rapidly outside of it. The "Deacon Alien" was impregnated in an Engineer by the Trilobite and then born almost fully adult, with no explanation as to why. What was accelerating their growth?
THEORY: THE ENGINEERS WANTED TO KILL HUMANKIND BECAUSE THEY DISRESPECT LIFE
In many ways, for David (a synthetic being) to have the hubris to create life in Alien: Covenant laughs in the face of everything that the Engineers stood for. But can he be blamed, when he was built by a man defying his own life cycle by demanding immortality? Their entire culture is based on organic life, which they can't help but create. Their ships are alive, as are their weapons of mass destruction.
Fans have theorized that while the Engineers may have seeded humankind, they also sought to destroy it once they realized how little regard humans had for their own lives.
MAKES NO SENSE: BLACK SPACE GOO
Prometheus revealed that the Engineers, the ancient ginormous humanoids from LV-223, created the xenomorphs by experimenting with black goo. The black goo is the mysterious substance that seeded many creatures in the galaxy, apparently.
It seems to react differently depending on what it comes in contact with. Apparently, the black goo can create "infected" humans, who can create Trilobites by having intercourse with a normal human. These are suicide creatures born from a human female - imagine giant Facehuggers. If they attach themselves to a regular human, then you get a "Deacon Alien."
THEORY: DEACON ALIENS BECOME QUEENS
According to Prometheus and Covenant, if a Trilobite attached itself for oral implantation to an Engineer, a "Deacon Alien" would emerge. This is a prototype of one of the very first xenomorphs and shown to be rather large in Prometheus.
Fans believe that it's the "Deacon Alien" strain that would become a Queen Alien, and able to lay the eggs that appear in Aliens. The Queen is the largest of the xenomorphs, and others of the species have only previously been classified as "Warriors" and "Drones" later in the franchise.
MAKES NO SENSE: WHY THE COMPANY NEVER LEARNS FROM ITS MISTAKES
In the future depicted in the Alien franchise, "The Company" is a somewhat nebulous authoritative organization later referred to as "Weyland-Yutani" (though the logo could be seen on various paraphernalia and props). Even after that incident concerning the crew of the Nostromo on LV-426, The Company wants Ripley to go to a jeopardized colony rather than nuke the planet from orbit.
In the Alien universe, the Corporation wants to capture and study xenomorphs even after the entire colony is wiped out and they wipe out an entire research vessel and threaten Earth's entire population. Surely, there must be more to it than The Company considers them "magnificent specimens."
THEORY: DAVID DOESN'T WIPE OUT ENGINEERS
In Alien: Covenant we learn that the android David took an alien ship and went on a mission to seek out the Engineers on their homeworld. When he arrived, he used their own black goo against them as a weapon of mass destruction, killing all of them as they went about their business.
Fans have theorized that the beings he wiped out weren't the original Engineers at all. Though they're tall and have the same hypertrophied features as the Engineers, they live in rudimentary dwellings and wear simple rags. There are temples on the planet, indicating the inhabitants worship some sort of deity. They hardly seem the beings that kickstarted all life in the universe.
MAKES NO SENSE: HOW DID AN ENGINEER/SPACE JOCKEY GET ON LV-426 IF THEY'RE ALL DEAD?
If the beings that David wiped out were engineers, then they'd all be dead, and there'd be no giant space jockey to appear in a derelict ship on LV-426. That ship, Engineer, and those eggs are also thousands of years old. Why does it have the eggs?
Furthermore, the Space Jockey from Alien is enormous. It's much larger than the Engineers by a good 20 feet. In that film, it was clearly a desiccated, rotting corpse with skeletal arms, eye-sockets, etc. In the script for Prometheus, much of which was not included in the film, it explains the Engineers may have descended from an older, larger race.
THEORY: THE COMPANY SENT RIPLEY ON PURPOSE
Fans have long suspected that there was something special about Lt. Ellen Ripley, beyond her obvious smarts, integrity, and ballsy determination. They believe that Weyland Corp not only knew about the xenomorphs on LV-426 but knew there was something special in Ripley's DNA that made her a special candidate for impregnation.
The only person/survivor to know about the location of LV-426 would have been David, who also had knowledge of the xenomorph life cycle. It might also offer a clue as to why The Company always needs Ripley's help, but never wants to listen to her about fully destroying the alien.
MAKES NO SENSE: ALL THE RANDOM CREATURES IN PROMETHEUS
If you're trying to follow the life cycle or gestation of any of the creatures in either Prometheus or Alien: Covenant, it can be difficult to keep track. The black goo is arguably at the center of their creation but in a multitude of ways. Humans can be impregnated by intercourse, direct injection, and apparently interacting with a "hammerhead" that swims around pods like an aquatic Chestburster long before they release a Facehugger.
Not only that, but the giant tentacled Trilobite is born from a human female. Why does it not take on more mammalian features? Why is it so big? When it attacks an engineer, the Chestburster that eventually erupts from him is a fully grown xenomorph. Even after Alien: Covenant, we still have no idea how the xenomorph will streamline this process of impregnation, incubation, and growth.
THEORY: DAVID TRIES TO REVERSE-ENGINEER THE XENOMORPH TO WEAPONIZE IT
It's been said by fans that not only was David attempting to reverse-engineer the Engineers' experiments to create the "perfect organism," aka the xenomorph, but that he would utilize them as bioweapons to take out humanity (which he saw as an imperfect species).
Fans further theorized David made it back to Earth, took over Weyland-Yutani, and eventually was behind the development of the Ash series of android that he would send with the Nostromo to protect the alien eggs on LV-426. Although why he would send a ship to LV-426 when he had the ability to create neomorphs is anyone's guess.