First of all let me apologize but the information presented here will likely be difficult to follow for anyone who is not well versed in Drakengard/Nier lore. For those of you who know what I'm talking about this should hopefully all make sense to you. Unfortunately for me to go in detail and explain exactly what I'm referring to would probably result in a 300 page google doc and at that point you might as well just research everything yourself.
Secondly, this theory contains SPOILERS for Nier, Nier: Automata, Drakengard, and Drakengard 3. In the event any of this turns out to be true, then this could also be considered spoilers for the Nier raid itself. If you don't want to be spoiled then turn away now.
Thirdly, let me just state this post is simply meant to be theorycrafting for FUN. It is entirely likely that none of this is correct. I'm simply posting to share my thoughts with the community and discuss the potential implications with everyone.
So with that out of the way, let's get into the theory. Which I will break into two parts.
The first is background theorycrafting for Nier: Automata. It contains information which is heavily implied but not straight up confirmed through any known source. It is a theory which has been derived from factual information which can be found in multiple sources, including the games themselves, various novellas and short stories written by Yoko Taro, the YoRHa stage play, the Grimoire: Nier companion book, Yoko Taro interviews and timelines in various artbooks, etc ...
The second part is speculation and educated guesses based on Nier and XIV lore which could link the two games together.
Part 1:
Theory: Data from the Gestalt Program including data of Nier himself (the original gestalt aka Shadowlord) was copied and uploaded to computer databases as a safeguard in the event the gestalts could for some reason not rejoin their replicant bodies. This data was eventually incorporated into the machine network accessed by machine lifeforms.
Through accessing this gestalt data, the machines began to incorporate the will and desires of humanity into their own logic until eventually, data from each and every gestalt that existed during the gestalt program was incorporated into an individual machine lifeform. Thus humanity was reborn as machines. Utilizing the machine network, machine lifeforms were able to overthrow the alien invaders out of a desire to reclaim the earth for humanity.
In much the same way as the gestalts that were used to create the 13 grimoires, gestalt data which was incorporated into machine lifeforms allowed for some level of magical prowess. This is how the machines were able to create Adam and Eve and why they take on the appearance of humans. When presented with the threat of 2B and 9S eradicating their community, the machines were able to pool together their magical energies in an act of desperation to summon forth guardians to protect them (the same power used by the intoner sisters in Drakengard 3). The guardians took on the form of the humans which summoned them. This is also why the symbol of the Cult of the Watchers appears on Eve's body. He was created using magic. All magic on earth originates from the flower that the intoner sisters were born from and was eventually passed down through the Cult of the Watchers which was founded by One's male clone.
YoRHA black boxes are made from machine lifeform cores. By utilizing these cores, YoRHa units are effectively joining their own consciousness with that of a human gestalt. This is where the YoRHa units "false memories" arise from. In essence, the YoRHa become the remnants of humanity along with machine lifeforms. They were fighting to save that which they themselves had unknowingly become. The truth of the lie that had been perpetuated then becomes an even worse lie.
The theme is very much similar to that of the original Nier in which Nier unknowingly dooms humanity doing what he believes is the right thing to do. By fighting for what he believes to be his daughter Yonah, Nier initiates the breakdown of Project Gestalt when he rejects the Shadowlord as his true self and destroys him. An act which he perceives will save Yonah's life, but in reality causes the relapse of her gestalt along with every other human gestalt left in existence. The YoRHa similarly believed they were fighting on the behalf of humanity. In reality, they were destroying the very humans they were trying to protect, while also failing to realize that humanity existed within themselves the entire time.
In the end of Nier: Automata, the data on machines, androids, and humans (effectively all 3 are one in the same at this point) was launched into space to unknown effect. This leads into XIV theory.
Part 2:
XIV tie in theory:
The data which launched into space is eventually recovered by a hyper-intelligent alien race which is engaged in a war with a race of space dragons (This race eventually becomes the inhabitants of XIVs "Dragonstar" and also the dragons which exist in Drakengard series.). The aliens use the data to recreate YoRHa androids in an attempt to use them in the war against the dragons. These androids possess the wills and desires of humanity as well as magic of the Cult of Watchers due to the incorporation of gestalt data.
Within Nier/Drakengard lore exists the potential for branching dimensions and timelines due to the occurance of "Multiple Worlds Divergence Phenomenon". Which states that: when a group of "singularities" (most commonly special sentient beings) come together, splits occur in a timeline of events. This occurs in the original Drakengard when Angelus the dragon comes into direct contact with the Queen Beast.
When these dragons come into contact with androids, a Multiple Worlds Divergence occurs resulting in 2 separate timelines. The first is the timeline in which androids and dragons along with the Cathedral City arrive in Drakengard 3. The second is a timeline in which androids and dragons (and probably also the Cathedral City) arrive in XIVs universe. In the XIV timeline of events, dragons go on to populate the Dragonstar. In both timelines, androids go on to record history from the shadows and remain unnoticed, simply blending in with normal humans.
From here there's not much else to go on to continue to speculate down the XIV timeline of events. But using the above mentioned scenario we can assume a few things which could have implications for the raid storyline.
1. Androids have always existed in XIVs universe since probably before the fracturing of Hydaelyn.
2. With the existence of androids its likely that the machine network is also operational in XIVs universe.
3. The logic virus / red eye disease probably also exist in XIV universe.
4. Within the machine network exists the data for (Nier/Shadowlord) meaning it's possible for the Gestalt Program to be recreated in XIV universe.
5. Data for all Nier characters should exist on the machine network, including 2B, 9S, Adam, Eve, Emil, Kaine, Yonah, etc.
If I were to speculate further, I can imagine a scenario where the Garlean Empire learns of the existence of the machine network and uses its information to recreate the machines from Nier: Automata. Androids are then forced to reveal themselves in order to combat the threat. Androids containing 2B, 9S data appear, etc, etc.
Addendum:
I wanted to take a bit of time to clarify a couple of things that may be unclear in this post.
1.Why is part 1 of the theory necessary for part 2 to occur ?
-In order for the multiple worlds divergence to occur, it's important that a dragon comes into contact with a sentient being which possesses magic of the Cult of the Watchers. So it's necessary to explain how that could possibly happen. The answer is the androids contain data of human gestalts which possess such magic. Data that might possess potent enough magic could include, Emil, Nier/shadowlord, Kaine/Tyrann, Adam/Eve, etc...
2. What do you mean exactly when you say "The truth of the lie that had been perpetuated then becomes an even worse lie." ?
-The main plot of Nier: Automata involves discovering that there are no humans on the moon and the entire YoRHa program was a lie. So the "truth" of this lie is that humans no longer exist and have been extinct for some time. This causes the androids to believe that they have no reason left to fight, or to exist at all, as their sole purpose for existing in the first place is to eradicate the machine lifeforms on earth in order to reclaim the planet for humanity. However, according to the theory I've presented, that truth then also becomes a lie. This is because the machine lifeforms and indeed the YoRHa androids themselves, are all host to human gestalt data that had been copied from the original Gestalt Program. So the real truth is that humanity is alive and have already reclaimed the earth for themselves after slaying their alien masters. So the "truth" that humans are extinct becomes an even worse lie. Throughout the entire game, the YoRHa androids are killing the humans that they are trying to protect. Every time they kill a machine lifeform another human life is extinguished. To add insult to injury, the machine cores which make up the black boxes of YoRHa units also contain the data of human gestalts. Therefore the bodies which YoRHa deems to be expendable, as they can simply upload the androids' personal data into a new body, actually contain human life as well. So every time the androids replace their bodies and/or detonate their black boxes, another human is killed in the process. This is the same as the original Nier, where Nier is unaware that the shades he has been killing the entire game are actually all human gestalts.
3. Evidence for the existence of the "Hyper-intelligent race of the future".
- The simple answer ? Accord, the android from Drakengard 3. While it is never explicitly stated what her role is exactly in the greater Drakengard/Nier universe, we know that her mission broadly is that she was sent to observe the events of history and report back to some unknown entity via the use of a special phone. Specifically in Drakengard 3, her target for observation is Zero, who she refers to as the "singularity". From this we can infer that she must be referring to the "singularity" which caused the Multiple Worlds Divergence which resulted in the Nier timeline of events. Therefore it is assumed that Zero eventually becomes the entity known as the Queen Beast. This is implied during the final battle of Drakendgard 3 ending D, where you're flying around as Mikhail doing a rhythm game against a bunch of grey giants modeled after the 5 intoner sisters. This exact same rhythm game reappears during the battle with the Queen Beast in Drakengard 1. Additionally there are scenes where Accord seems to have knowledge of the existence of multiple timelines, and even uses her phone to call in "interventions" in the timeline when necessary. Therefore we can conclude that Accord is cooperating with the so-called "Hyper-intelligent race of the future" and that they have the ability to oversee and influence events throughout time. The fact that dragons, Accord, and the Cathedral City all appeared at the same time and from the same place suggests that they all originated from the same point in the future. The fact that this race and dragons are engaged in a conflict is merely a best guess on my part. An argument could be made that this advanced race may be the same race that created Omega Weapon.
4. Evidence Drakengard dragons, and XIV dragons are the same race.
-In Drakengard 3 during the prologue, the dragon Michael is killed. Later we see that Michael has reincarnated as a child. The only explanation we are given for this is that Michael's dying wish was to be reborn so that he could continue fighting with Zero. This suggests that dragons have the ability to reincarnate at will. This same ability is demonstrated by Midgardsormr at the end of ARR storyline. It is only out of a desire to test the Warrior of Light that Midgardsormr chooses to reincarnate and is reborn as a child version of himself. It could also be suggested that Drakengard's "Pact Magic" is at play when Midgardsormr binds himself to the Warrior of Light. The price for the pact being the Blessing of Light. This is reinforced by Midgardsormr's dialogue in The Rising Chorus: Scene 3, where he states "Thy covenant binds me to thee".
The Mindblowing TLDR parts:
1. The dragons in Drakengard and in XIV are the same race of dragons.
2. Androids have always been in XIV hiding in plain sight.
3. The event which caused the Cathedral City to appear in Drakengard 3 is the same event which caused androids and dragons to exist in XIV.
4. The machine network exists in XIV and is older than the Allagan empire. Allagans could have used this to develop their technology.
5. The race responsible for sending Accord to the past to monitor history in Drakengard 3 may be the same race that created Omega weapon.