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A Xenomorph will fight the Neomorph
Since it's been confirmed that a new type of alien lifeform will appear in "Covenant," it's very likely that the classic Xenomorph will get into a fight with it at some point, and though the battle will be very close, the Xenomorph will eventually triumph.
  • Jossed; both Neomorphs die before David adds his 'missing ingredient' to his experiments - introducing human subjects to the classic egg/facehugger.
    • Not exactly. A Neomorph/Xenomorph fight did occur in an early draft of the script and was retained in the novelization.

In The Stinger, Samus will appear.
Weyland-Yutani hired her services. She will blast a surviving Xenomorph before the credits roll, and get ready to single-handedly bring extinction on them in the sequel.
  • Jossed.

David will be the film's Big Bad
  • Pretty much confirmed. As it stands in this point in the narrative, David appears responsible for the entire Xenomorph threat.
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The film will have a subplot of David vs. Walter
Considering they're both versions in the same line of androids, David descended into dark experiments involving the Xenomorphs while Walter is still a (seemingly) loyal ally to the crew of the Covenant. This would suggest that the two will come into conflict at some point; this may result in Walter ending the threat of David for good, and/or Walter being somehow inspired by David to follow his predecessor into villainy.
  • Confirmed. David is actively responsible for the overall creation of the Xenomorph - or so it appears at this point in the series - and he and Walter come into conflict when his designs actively threaten and harm the Covenant crew. Walter appears to die remaining loyal to his crew, usurped by David.

The predators will appear
Making the Alien vs. Predator series canon again.
  • Jossed.
    • It's always been canon, just a separate canon.

Elizabeth Shaw is not dead, but suffered something worse on Paradise...
Whether it'll be the black goo or David's machinations, she was mutated into some sort of alien birthing machine, like a precursor to the Xenomorph Queen. H.R. Giger, the inspirational source for the Alien franchise design, has paintings of a woman's head surrounded by biomechanical tubes as well as a woman attached to a machine.
  • Toyed with. Shaw's corpse is reflective of some of Giger's drawings if not directly referencing one of them, and she appears to have been an initial subject for his experiments.
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A human will become the Neomorph
Specifically, the guy undergoing the "backburster" sequence in the trailers.
  • Jossed. The Neomorphs are grown from the results of David's black-goo tinkering interacting with human subjects.

This is how the trilogy will go and end

According to Ridley Scott, the trilogy will eventually link up to the original Alien. I believe this is how it will go. During the ending, Davis has taken control of the Covenant and sets course to its original destined planet. Obviously, David will take the time he has to experiment on his unwilling test subjects in order to perfect the Xenomorphs. By the time the next batch of protagonists arrive, he will be close to completion. His final experiment will involve a Xenomorph Queen (which will then kill him afterwards).

Because the first Alien had the protagonists of that film discover Xenomorph eggs on an engineer spaceship, I will believe that one of the last (or THE last) of the Engineers will arrive and take some of the eggs with them. I believe that one or more of them will discover that it was David who destroyed their homeworld, and they will try to seek revenge by traveling to Earth with the intention of unloading all the eggs and infecting the entire populace. However, since the Engineer we see during the first Alien movie had his chest bursted open, I have a theory as to why:

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One or more of the protagonists of (possibly) the last movie of the prequel trilogy will have snuck aboard the Engineer spaceship and knowing of the Engineers intentions, they will try to stop them. However, rather than facing an Engineer, the one piloting the ship was possibly infected by a facehugger, and knowing that his time is running out is determined to arrive on Earth before the chestburster erupts from his chest. Obviously failing to get to Earth in time. The Engineer Xenomorph then attacks the protagonists, chasing them around the ship and the protagonists somehow send the mysterious transmission during the first film. The last film will end in a somewhat bittersweet ending which will have the protagonists sacrifice themselves to kill the Engineer Xenomorph but at the cost of their lives (likely death through airlock).

  • Alternate theory - By the end of the series, David will either end up in control of Weyland-Yutani or at the very least much of his knowledge will end up in their hands, thus leading to the corporation's endless obsession with the xenomorphs in "later" films.
    • Building on that, David may actually be directly responsible for the events of Alien and Aliens. He's not so much in control of the company as manipulating it to destroy humanity via the Long Game. Through Covenant, he has a backdoor into Weyland-Yutani and could easily spoof or forge messages. Ash could actually be one of David's followers or someone he reprogrammed. That would explain why the board of inquiry in Aliens didn't believe Ripley's story and the lack of evidence and data; not because of a coverup but because the company didn't know. David might even had been the one to send Burke the coordinates to the Derelict on LV-426.
  • Alternatively, David returns to LV-223 to hijack another Engineer ship, restock on the Chemical A0-3959X.91 – 15 pathogen, and carry the Xenomorphs to Earth. David modifies or upgrades himself — possibly with Engineer tech — into a sort of biomechanical cyborg in order to surpass his creator's vision of him, but in a delicious, karmic twist of irony he winds up a victim of his own creation and crashes on the nearby LV-426, dying to give birth to the first of the classic biomechanical Xenomorph strain seen in the original quadrilogy, which matures into a Queen and fills the cargo hold with eggs. This would possibly explain why the prototypic Xenomorph seen in Alien: Covenant is more organic than the classic version seen in the quadrilogy.

Facehugger timing
According to this film a few seconds after a facehugger is attached, an embryo is implanted, seemingly making the extra hours they stay attached in other films pointless. However, perhaps the embryo IS implanted in the first few seconds in other films, with the remaining time being the facehugger not only keeping the host alive, but also feeding them nutrients/chemicals to promote healthy xenomorph growth.

That said, in Aliens the guy who died having the facehugger removed didn't host a chestburster... as far as we know!

David lied about creating the Xenomorphs
Here are all the lies he told.
  • He lied about how the Engineers died.
  • He lied about how Elizabeth Shaw died.
  • He lied about his feelings for her.
  • He lied about the safety of "his" experiment.
  • He lied about which android he was.
  • He lied about what happened after the solar flare.

Why should we believe any word coming out from his mouth to be true? The Xenomorphs were actually created by the Engineers thousands of years ago, he just used them for his own purposes.

  • As a corollary: Alien vs. Predator is still canon.
    • Jossed; Word of God has already confirmed that David is responsible for the Xenomorphs. There's nothing, however, stopping them being based on projects David may have seen in the Engineers' archives, and there's no reason the better Av P material can't be canon, given that takes place later on; we've just had two movies of dubious quality removed.
      • They're not removed, they're simply a separate continuity now. Remember, there was an Alien skull in the second Predator movie si it seems Alien vs Predator is soley in continuity with the Predator series.
  • David didn't create the original xenomorphs, they existed in the past based on murals in the room with the goo and dead engineers. He re-created them (imperfectly, since these don't quite look like the ones seen in previous films, they lack the biomechanical look), based on research notes he found, and experiments with Shaw and various life form with the goo.

Walter survived, and will potentially return
This is an extremely optimistic reading of the film but. Walter was probably built to withstand a lot more than David was - while David was on a science/exploration ship, Walter was on one that contained heavy machinery meant for terraforming and creating a new colony, which may mean that he is generally more of a "labourer" android than David. Since we never get overt confirmation that David killed him, only that he is impersonating him, it's possible that Walter may leave the same way David got there, with an Engineer ship - and chances are, with his loyalty to his crew and specifically to Daniels he will be none too happy if/when he meets David again.
  • That may explain how they ship from the original movie ended up where it was and full of eggs.
  • He could possibly get that crashed ship flying again to give chase, or more likely find another one somewhere on the planet.

David's behavior in this film is the result of a Three Laws-Compliant violation
Okay, David isn't exactly Three-Laws Compliant even in Prometheus (he seemed to have no trouble setting his creator up to die and experimenting, probably lethally, on Holloway), but he's at least got some kind of behavioral inhibitors. And as we know from Prometheus, the Engineers were planning on wiping out humanity. David has to try and protect humanity, and the only means he has to do that is the Engineer's own bioweapons, which will kill all of them. Now, here's the catch. . . Prometheus also tells us Engineers and humans have the exact same DNA, which means that Engineers could be considered "human." David mulls this conundrum over and over during the trip to Paradise, and finally comes to the conclusion that he has to destroy the Engineers to save humanity, even if that means killing other "humans." It's the final nail in his behavioral inhibitors breaking completely, leading him to become an Omnicidal Maniac. Or, he calmly explained his plan to Shaw when he woke her up, she didn't go along with it, and his already-damaged inhibitors didn't stop him from killing her to stop her from interfering in his plan (notice Shaw's absence during David's flashback about bombing the Engineers), and that caused him to snap completely.

The Nostromo is an even older exploratory vessel converted into an M-Class Starfreighter
The reason the Covenant appears to be more advanced than the Nostromo despite events taking place a couple of decades before Alien is due to the Nostromo being built earlier than Covenant. The Nostromo was an exploratory vessel that was converted into a freighter. The Covenant is a colony ship, and therefore contains everything the colonists need to build a colony, including advanced imaging and surveying equipment. The Nostromo's appearance, state of repair and supposedly outdated technology can be explained away by her role. Its purpose is to simply haul loads from one planetary system to another. The crew only need to be awake shortly after departure and shortly before arrival. Therefore, they don't need all the bells and whistles Covenant has, nor would there be much of a priority to fix non-essential equipment. Even Dallas had cut corners on repairs in a rush to get off of LV-426, leaving some equipment broken. Airliners and Cargo Ships are typically used for 20-30 years before scrapping them (Great Lakes haulers can last up to 100 years), maintaining and updating them as needed. Spacecraft would be built to last under even harsher conditions for much longer.
  • That does make sense, as the Nostromo was specifically noted as an ore hauler. A ship of this type would have the minimum of everything, so that a profit could be made even with a load of low-grade ore. Compare this with container ships of the modern age, most of the ones in service are at least 30 years old.

Spoilers: Alien as The Bible
When Ridley Scott confirmed that the reason why Engineers consider us failures because we killed Jesus Christ who was an Engineer, inevitably theological parallels were inevitable.
  • The Engineers are obviously Jehovah, and Black Goo is like the Fruit of Life. In the right hands (the divine) it is a force of Creating Life; in the wrong hands it is a Pandora's Box, such as what happened with...
  • Humanity. We were created and gifted with intellect and emotions, and were given a star map, because we were their children. As such, a select few of the best Engineer specimens (such as the perfect-statuesque bodybuilder from the prologue, aka "Prometheus") commit ritual suicide to trigger evolution in planets and create the next generation. The intention was for them to evolve on their own, but got sabotaged when Humanity turned to other, more jerk-ass False Gods such as...
  • The Yautja, aka Predators (yes, AVP is still canon) who are mortal enemies of the Engineers (perhaps a failed creation? A tribal species that stole Engineer tech?). So, there were these Predators, who were tired of hunting the most difficult sport in the universe, so they stole Engineer technology, and found out about the Engineers' children...
  • The Engineers attempted to take back Earth but it was too late as humans now worshiped Predators as false gods (aka the Nephilim) and adopted their violent, tribalistic ways (the Fall of Man. No, the Serpent is not Lucifer, that was in later tradition). This is where Noah's Flood comes in in the form of the Goo as no longer an agent of divine life, but a weapon of mass destruction and a plan to use their own obsession with sport hunting against them. They tricked the Predators into taking a deadlier animal than humans...
  • Thus the creation of the first Xenomorphs, initially nothing more than a plague, an instrument of God's wrath. In the end of AVP's flashback, the Predator base in Antarctica was flooded by a Zerg Rush of Xenos, wiping out traces of civilization there. This is where we get the legends of Atlantis from. However, for the Goo to create these Xenos, humans had to be sacrificed.... so they let all the Predator worshipers die under the xenomorph plague and spared a few such as Noah, and because the xenos at that time were nothing but animals, they died off more easily (AVP aliens are way easier to kill than classic Aliens). Humanity forgot the Predators as they repopulated the world, and the Engineers made a Covenant that they would no longer deploy divine retribution to the world again. That's why they made murals of Xenos so that they won't forget how they almost killed their children off.
  • Humanity has progressed enough but lingers of tribal conflict in the form of violent nationalism remains. So they had an Engineer inseminate a Human... the result being Jesus! Jesus roamed the world in 40 days and returned back as a prophet to teach that humans need to give up their tribalism and fulfill the Covenant i.e. ascend as another Engineer race. Instead we got the Passion of the Christ. This is the moment that answers Shaw's question "Why do you hate us?": Mankind killed off one of them, and since Shaw was a devout Christian (which made the Engineer suspiciously offended before touching David), they are now following a cult glorifying an Engineer being tortured to death!
  • Mankind, therefore, has become like the Predators: a violent, lost race now with space travel. The most interesting thing is how the Engineer was triggered by touching David as he was a synthetic android, and also immortal, who now tells him that Weyland wants eternal life from him. In other words David is an example of this failed species now committing the ultimate sin: Creating Life, a power only reserved for the Divine. So, the Yautja are just an external factor of pagan spirits, and if the Engineers are God, then Humanity are Angels, specifically, fallen angels. In other words, You are the Demons.
  • The Antichrist is obvious: the AI with the God Complex aka David!
    • David, a mere creation to serve humans, is prided by Weyland to be perfection incarnate. And as time progresses he becomes more arrogant. He prides himself on his Wicked Cultured knowledge especially in world literature (presumably Paradise Lost and the Bible will be included in his list of readings, was humbled by Walter pointing out the Ozymandias poem was not from Lord Byron), thinks himself as more perfect than his creator (the dying Weyland) and has an inclination of killing the Creators (including the franchise's resident God, the Engineers), so why not for him to have a rather Luciferian role in the greater scope of things? You would almost expect him to quote Nietzsche and proclaim God Is Dead.
    • It was the Engineers who conceptualised the Xenomorph as nothing more than bioweapon, but it was David's unholy experiments with Creating Life, especially his genocide of Engineers and perverted use of Shaw as an Alien Queen, that resurrected this Beast of the Apocalypse into an abomination much worse and deadly. Unlike the previous animalistic Xenos, David's daemonic creations now possess both the superior biology of the Goo, and Human Intelligence from his experiments with Shaw and the Engineers (e.g. the Alien in the first film was capable of human things like even rape); this Alien now holds both the Fruits of Life and Knowledge, the only thing it needs is mechanical components to become immortal and thus perfect; and who better than the one who sought to be God, aka David himself? He uses Engineer biotech to merge himself with the beast, completing its biomechanical components.
    • As for the Antichrist controlling the world from the shadows, we know from Covenant that David has access to the backdoor of the main Weyland-Yutani Mainframe. Also, Alien-cultists like the android Ash still exist. Who knows if parts of David still survive in Earth's computer systems, manipulating mankind into a suicidal obsession with Xenomorphs?

David, Elizabeth, the experiments, and their relationship
"The Crossing" prologue video that's narrated by David, as he talks about his journey with Elizabeth to find the Engineers' home world, depicts an almost convivial and tender relationship between the two that is very much at odds with David's later murder and dissection of her. Of course, we only have David's word that the events of the video happened as they did and he very well might have been bending the facts or straight up lying. This of course calls David's feelings for Elizabeth into question - he claims that he loved her, but says this in the midst of a whole pack of other lies he told Walter; however, he also did create the headstone for her in a beautiful garden when he really didn't need to, and when Walter happens upon him later with her picture, David was playing a song for her on his flute and crying, which he probably couldn't have put on for his "brother's" benefit since he didn't know he was going to be interrupted. There is also the matter of David's other drawings, which depict Shaw as a bio-mechanical queen of sorts (the last one especially, and it even looks sort of heart shaped).

The answer to it all: David does love Elizabeth in his own deeply sick and twisted sort of way. Perhaps David did kill her (or maybe she perished by some other causes). And through a combination of his massive god complex and Love Makes You Crazy, Love Makes You Evil, Mad Love and whatever else, David began using Elizabeth's genetic material, combining it with the Engineer's black goo, tech and whatever else he could get his hands on to create the children they could never have together and "immortalize" his beloved. This "seeing the aliens as his and Elizabeth's children" thing is especially apparent in the scene when David becomes furious (if not downright heartbroken) when Oram shoots the neomorph to death.

Covenant is set in the same universe as Idiocracy
That would certainly explain a lot.

The film quoting Ozymandias is an indirect reference to Frankenstein
The writer of Ozymandias is Percy Bysshe Shelley, the husband of Mary Shelley, the writer of Frankenstein. This theory may seem slightly weird to some people, but think about it. David can easily be seen Dr. Frankenstein, while the Xenomorphs can be seen as the monster. Also, isn't it interesting that this is a sequel to a movie called Prometheus, while one of the alternate titles to the novel is "The Modern Prometheus?"
  • On second thought, I'm honestly not sure if the whole Ozymandias thing adds to my theory at all, but I'm keeping this theory here since I'm still proud of the Frankenstein similarities.

Each film in the prequel series will be named after a ship
First, we have the Prometheus, now we have the Covenant. I think about the only thing that can really refute this is the announcement of the next film's title.note 
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