One question many people keep asking is whether or not Alien: Covenant will address what happened to the Deacon on LV-223 following David and Shaw's departure in Prometheus. The Deacon refers to the Alien creature which birthed from the Engineer following his battle with Shaw's baby, the Trilobite.
Will the Deacon be in Alien: Covenant?
The simple answer to that question is no. However, the Deacon has not been forgotten entirely for the Prometheus sequel.
Alien: Covenant takes place on a very different world, far away from LV-223, the moon which housed the Engineer installations and which now houses the Deacon. Concept art from Prometheus shows the Deacon emerging from the crashed life boat where it was born and actively searching / investigating the surrounding landscape.
This of course takes place after David and Shaw have departed for Paradise, so there is no chance the Deacon managed to sneak aboard their ship prior to their departure.
What happened to the Deacon?
Ultimately, nobody knows. However, LV-223 is home to many more Engineer installations like the one the Prometheus crew discovered. These installations each house a Juggernaut ship and a payload of Black Goo and we can also assume that they contain similar storage caverns with biological materials, tombs, etc...
The Deacon is likely incapable of using the Engineer technology, so it will essentially be stranded there until someone or something comes by and offers it a way off-planet.
We also don't know if any other Engineers survived in cryo-stasis in any of the surrounding installations. If any did, they could provide a viable host for the Deacon to use for procreation, assuming the Deacon is capable of egg-morphing like the Xenomorph.
Keep in mind as well, the Hammerpedes (mutated Black Goo worms) are still alive and well, too. How the two species will interact is unknown, but it is speculated that the Hammerpedes lack the ability to seed hosts like the Facehugger and so would not likely attempt to attack or impregnate the Deacon.
The Deacon has been acknowledged in Alien: Covenant's marketing
On the viral website AlienMovies.com, a MUTHUR interface has been constructed and allows fans to input questions to which MUTHUR may give a direct answer or come back with an error, unable to compute. Many of our members here have discovered quite a few interesting reaponses already.
Upon entering the code name Deacon, MUTHUR responds with a fairly detailed description of the Alien, but no information on its whereabouts or fate is displayed.
In Scott's original Alien, MUTHUR represented the Nostromo's link with the Weylan corporation. If we are to treat the viral website interface the same as how it was represented on-film, it would suggest that Weyland-Yutani are in fact aware of the Deacon and have data records dedicated to its existence.
Will we ever see what happened to the Deacon?
Considering Ridley Scott and Fox have at least two more sequels to Prometheus planned, it is absolutely possible that the Deacon's fate will be explained at some point down the line. It is also possible that the Deacon plays a much larger role than we initially thought and is eventually discovered by another exploratory vessel in deep space. Surely Weyland-Yutani will wish to know what became of their Trillion-dollar space craft.
So, ultimately fans should not expect to see the Deacon in Alien: Covenant, but they shouldn't lose hope either. With a total of 4 films planned for this Prometheus saga, the liklihood of the Deacon's fate being explored is extremely high, if not on-film at least in written publications or comic books.
What's your best guess for what happened to the Deacon on LV-223? Let us know your theories in the comments section below!
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