This theory explores the following thought experiment: If the Zonai and Twili were directly related, HOW would they be related?
I will try not to fluff up what I am talking about in this post. I will be assuming the following two things:
1. The Twili and the Zonai ARE directly related.
2. The Wild Era's Hyrule is a refounded kingdom. (I will address True Founding later, but it's complicated address both at once)
I will state my conclusion first then address the logic after:
The Zonai are the future form of the Twili. The Interlopers were a rogue faction of the Sheikah just like the Yiga are. After being banished to the Twilight Realm, they underwent a spiritual rehabilitation process that allowed Hylia to later reintroduce them to Hyrule as the Zonai. The Twili both physically and spiritually were transformed by their time in the Twilight Realm and the physical form of the Zonai reflects the form of their spirit.
Why the Interlopers were probably rogue Sheikah
The first point I want to address on this topic is how there is already an obvious precedent for this happening: The Yiga Tribe.
We were introduced to the Yiga in Breath of the Wild and were notable as the first explicit example of evil or rogue Sheikah, something that people speculated may have happened but not something established with lore yet. With the precedent that the Ancient Sheikah could splinter into the Yiga, we retroactively have the justification we need to presume the Interlopers were of the Sheikah Tribe.
There are some parallels between the Interlopers/Twili and the Sheikah as well. Before I get into those points, I want to address Twili magic. We see magic performed by both Zant and Midna in Twilight Princess. Zant's magic is known to be supplemented by Ganon's dark magic which takes on a color scheme of black, orange, and red. Midna performs some magic as well, notably near the beginning of the game when she releases Link from his chains, and that magic is also black and red.
However, if you look at the structures seen in the Palace of Twilight, the portals, and the bodies of the Twili, you'll see that a glowing greenish-blue color is present. In the Palace of Twilight, the light of the Sols activates doors and floating platforms. I think what this all indicates is that Shadow Magic (the magic of the Interlopers/Twili), utilizes the magic of darkness. However, the presence of this light on the bodies of the Twili in combination with the way the Sols interact with the Palace of Twilight indicate the Twili also possess this light energy as well. Keep this in mind for later.
Magic: Both Twili and Sheikah are capable of creating physical objects with their magic. With the Twili, we see this in the form of floating platforms primarily. With the Sheikah, we see similar feats with barriers or entire objects being created.
Symbolism: The Sheikah are obviously known for their third eye with a teardrop imagery. Though stylized, we can see exactly this imagery above the entrance to the Palace of Twilight
Affinity for Darkness: Although not something typically associated with the Sheikah, it is notable that in Ocarina of Time, the Sage of Darkness (Shadow in localization, but it's the same as Darkness) was Impa, a Sheikah. In the context of Ocarina of Time, there was an association of the Sheikah with the Shadow Temple and the dungeon beneath the well where people were apparently tortured. Exactly why the Sheikah were doing this isn't entirely clear, but their affinity for Darkness is clear even if that affinity is used to safeguard the world from the dangers of Darkness. As for the Twili, obviously there is an affinity for Darkness as well. The Fused Shadow, the artifact used by the Interlopers, contained a dark magic or spirit within it that had the power to corrupt other beings into monsters.
The Fused Shadow: This artifact is extremely fascinating. On the front, we see one eye that resembles one of the eyes on Majora's Mask. On the backside, we see an eye with a teardrop just like the Sheikah use. The Sheikah may or may not have any relation to Majora's Mask, but I think that the Fused Shadow is very much like Majora's Mask in that is houses a dangerous energy within it and is dangerous enough that it can corrupt otherwise good beings into evil ones. In a way, you could think of the Fused Shadow as Hyrule's Majora's Mask.
There is actually one more tribe that I have seen commonly attributed to the Interlopers, one that even I have entertained plenty of times: the Gerudo. This one is brought up for a couple reasons:
1. The Gerudo are also skilled with magic and are more typically antagonistic to Hyrule.
2. The Gerudo have red hair, and Midna and Zant have red hair or at least close enough to red to consider.
3. Zant's clothing has a Gerudo crest on it, even before meeting Ganon.
I think ultimately, the case for the Gerudo is simply weaker than that of the Sheikah. The Twili seem to have multiple men in their society. Zant is male, but as far as we can tell all of the regular Twili also appear masculine. Quite contrary to the Gerudo, the Twili appear to be a male dominated society if we are to take the Twili we can see as a representation of the Twili.
Additionally, the Gerudo are not associated with an eye and teardrop. They ARE associated with third eye imagery because a tradition involves a gem on the forehead, but the teardrop is still Sheikah-coded.
So, while the Gerudo may be the origin of the Interlopers, the Sheikah are a far better candidate.
The Corruption of the Sheikah
First, we must consider the point we just established: The Interlopers are likely former Sheikah.
Secondly, consider the nature of the Fused Shadow. It is a dangerous artifact capable of corrupting those in its proximity. It makes the people in its grasp wicked, and they can turn into monstrous forms.
And thirdly, consider the danger of being in the possession of the Fused Shadow, even in the context of protecting the world from it. The Fused Shadow is dangerous merely to be around. Without a person being aware, it can morph the demeanor of those around it and grant those people abilities (abilities gained through transformations like Fyrus) while under that influence.
With these points, I believe it is reasonable to conclude that, regardless of how intentional the usage of the danger Fused Shadow was, the Interlopers were likely influenced by the dark magic in the Fused Shadow and exacerbated the rebellion of these people.
The Twili's Rehabilitation
This point addresses the following question: Why would a banished faction of evil sorcerers become divine servants of the gods?
Let's look at a few perspectives.
1. The nature of the Twilight Realm and the Sols:
If you take the story of Twilight Princess at face value, you would be led to believe the Twilight Realm is merely a garbage bin. You throw a dangerous person in it and they are trapped there forever; it is a perfect prison.
In reality though, the Twilight Prison does not actually feel much like a prison. For one, it's not actually as closed-off as it appears. We are told the Mirror of Twilight is the only way in to the Twilight Realm, but Zant is able to leave the Twilight Realm before the story starts. You may assume Ganon's magic enabled Zant to do it, but the point remains that it is possible to escape the Twilight Realm with magic.
As for the Sols, their presence demonstrates that the nature of the Palace of Twilight is not of a prison. These Sols contain the same kind of Light that a Light Spirit bestows the land with and could be considered the Twilight Realm's Light Spirits. These Sols radiate an energy that powers doors, floating platforms, and switches within the Palace. Additionally, it transforms Shadow Beasts back into their Twili form.
These Sols purify the space around it of darkness, including the very Twili residing there. This purification is apparent by examining the visual design of the common Twili. Their actual bodies are a light blue but a black shadow covers most of their bodies. The portion of their light blue skin that is visible looks as if a light is revealing their skin; they are partially purified at this point.
2. The Twilight Realm as an "Underworld"
Early in the game, Rusl talks to Link about how the Twilight feels like the world of the spirits intersecting with the world of the living and how that time of day is when you can feel those lingering spirits the most. When Link finds Auru later in the game at Lake Hylia, he also characterizes the Twilight Realm as the Underworld.
I do not think the Twilight Realm is literally the Underworld in the context of the series lore, but the comparison to one is striking. It is no accident that the Twilight Realm is spiritual in nature. When the Twilight takes over Hyrule, its citizens aren't transformed into monsters but rather lose their physical form entirely and become lingering spirits.
In Buddhism, there is the concept of karma; the actions you take in life accrue positive and negative karma. When you die with negative karma, your soul is sent to a lower realm (Naraka) until that negative karma is used up and then being able to be reborn in a higher realm.
Think about the Twilight Realm as a plane of Naraka. The Interlopers aligned themselves with dark magic and were sent to the Underworld to use up their negative karma. Eventually, that negative karma will be gone and the Twili will be spiritually ready to be "reborn" or to join the World of Light once more.
While unconfirmed, something that strikes similarities to the Twilight Realm that has an explicit association with Hylia is the Silent Realm from Skyward Sword. This was a realm you inhabit with your spirit rather than your physical body. There are a few things about the Silent Realm that evoke thoughts of the Twilight Realm:
a. Association with spirits
When in the Twilight Realm (and without some kind of artifact to let you keep your body), you lose your body and become a spirit. With the Silent Realm, it is accessed by Link with his spirit. There is a teal glow to the body to indicate they are in a spiritual form and you can see it both on random people in Twilight Princess and on Link in Skyward Sword while in a Silent Realm.
b. Tears of Light
In Twilight Princess, Tears of Light are portions of the Light energy associated with a Light Spirit. When this Light is taken, it allows the Twilight to overpower it. When the Tears of Light are together, the Light Spirit's power is restored and the influence of Light becomes dominant.
It plays a similar role in Skyward Sword where they must be collected by Link and, when assembled, the Tears of Light suppress the guardians in the Silent Realm and allow Link to walk freely and obtain the treasure hidden by Hylia.
In both cases, the Tears of Light are associated with a peace free from darkness. For Link, it symbolizes enlightenment and the trials are honing his very spirit and dispelling any impurities/darkness from his heart. In the Twilight Realm, this process sort of happens to the Light Spirit and and that restoration dispels the Twilight from the land and returns the dominance of Light.
c. Dusk Relics
In Skyward Sword, Amber Relics can be found in many places and are magatama shapes. In the Silent Realms, Dusk Relics are found instead. These are purple and obviously associated with "Dusk" which is just another way to say "Twilight".
d. The "Hostile" Silent Realm
When Link touches the water in the Silent Realm, it activates the guardians who chase Link. When this happens, the entire color scheme of the realm changes from that blue/teal color to yellow/orange and the sky itself also changes to this color. It is in this phase when it most resembles the Twilight Realm which also had a similar color scheme with its sky.
Whether the Silent Realm is literally the Twilight Realm or not isn't really possible to determine, but there is certainly a case to be made that the Silent Realm was meant to remind us of it and in terms of the nature of the realms, there are definite connections to be made.
3. Pure Twili Magic
I think it is unclear exactly what kind of magic the Interlopers would have used while in Hyrule, but I think what is notable is the direction their magic is going during Twilight Princess. A unique trait about the Twili that is very rarely addressed is how the Twili are literally bursting with a greenish-blue energy. This color is very similar to the magic that Sol-infused technology glows with (doors, floating platforms, light switches), although is more green that the Sol's light.
If you think about the nature of Twilight Princess and its depiction of spirits as this green color, and the re-use of this color scheme in Breath of the Wild and Tears of the Kingdom, this green color is likely the color of Spirit energy. Therefore, we can see the Twili still are holding massive amounts of magical power. We also know the Sols explicitly drive away Darkness just like the Master Sword is known to do. Therefore, it becomes clearer that the Sols are purging Darkness from the Twili. This purification is visually communicated to the player via the design of the Twili.
I do also want to make a point to say I don't think the Shadow Magic used by the Interlopers is the kind of magic that the Twili would embody by the end of their purification; rather, it's the Light-aligned part of that Shadow Magic. If you think of Shadow Magic is a combination of Light and Darkness, the magic or energy the Twili would come to embody would be the Light portion of that magic.
Ultimately though, I think what is demonstrated here is the Twili have not been abandoned by the gods. The gods put the Interlopers in the Twilight Realm to be purified in a contained space.
If the gods chose to remediate the Interlopers back into pure beings instead of destroying or abandoning them, then perhaps there is a purpose behind that action.
The Re-Emergence of the Twili as the Zonai
In this section, I want to talk about the conditions around when the Zonai would've first appeared in Hyrule.
1. Physical and spiritual evolution of the Twili
There is an obvious question to ask when comparing the Twili and Zonai. The Twili are blue-skinned humanoids without much animal-like visuals (with the exception of Zant who looks somewhat like a snake, almost Voldemort-like). The Zonai, on the other hand, look like human-animal hybrids. How exactly are the Twili supposed to become the Zonai?
Let's think about the concept of Draconification for a moment. This is a process where a person ingests a Sacred Stone (a relic of the gods) and transforms into a dragon.
Now think to A Link to the Past's Dark World. In the Dark World, the corrupted Sacred Realm, the physical forms of mortals within it transform into a form that reflects that person's spirit.
Even in Twilight Princess, we see this concept used to make Wolf Link and Beast Ganon. These are forms that reflect the spirit of the person.
Now think to the Twili. They are bathed in the light of the Sols in the Palace of Twilight. Through the purification of their bodies, thanks to the Light of the Sols (relics of the gods), the Darkness in their spirits has been displaced and replaced with Light. It may be possible that, with the sacred Light of the Sols, the Twili come to adopt a form that reflects their spirit. Just as a person can ingest an unfathomable amount of energy and ascend to a dragon, a Twili could be exposed to so much sacred Light that they take on a new form as well.
In fact, we already know the Twili have undergone physical changes by the Twilight Realm because we know originally they were humans before being banished. Their time in the Twilight Realm transformed them into the modern day Twili. This transformation from the Twili to the Zonai would simply be one more step in the progression of the Twili.
If you think of the Zonai as being a physical form that reflects the "shape" of one's spirit, the connection to the Sheikah becomes even more clear, in my opinion.
One of the most curious things about the Zonai in terms of figuring out where to fit them in relation to the Sheikah, is how the Zonai literally have the Sheikah Eye as part of their body. It is not a tattoo; they have a literal third eye and a teardrop in their fur/skin.
Keeping in mind the Twili are former Sheikah and how they have been purified by the Light of the gods, ask yourself: What physical form would befit that of a true Sheikah, agent of Hylia?
My answer would be: The Zonai.
Allow me to present a piece of evidence for why the form of the Zonai reflects the spirit of a servant of Hylia/the gods:
An intriguing thing about Skyward Sword in hindsight of Tears of the Kingdom is the striking similarity between this particular guardian and the Zonai. Both wear similar clothes, have the same stature and silhouette including "ears", and are specifically associated with Hylia in a way that even the Sheikah aren't as they only exist in a spiritual realm. Compare the above guardian with Rauru and the Zonai statues found in the Temple of Light:
Many times when it comes to comparing visuals in the Zelda series, you kind of need to stretch a little to make connections. Sometimes it's swirls, eye designs, ear comparisons, etc. In the case of the guardians and the Zonai, there is not much of a stretch to be made at all. These are the same designs.
Either the Zonai were around prior to Skyward Sword, or the Zonai itself is derived either from those statues or from Hylia herself (because the guardians inhabit Hylia's Silent Realms). Which of these you adopt will depend on how you view the timeline, but focus on what is important here: The guardians are servants of Hylia.
Just as the Sheikah are Hylia's agents in the World of Light, the guardians are her agents in the Silent Realms, a spiritual realm.
Ask yourself one more time: What physical form would befit that of a true Sheikah, agent of Hylia?
2. The Intervention of the Gods
It is established lore that, for whatever reason, sometimes a Calamity befalls Hyrule without a hero present to destroy it. In Wind Waker, it was because the spirit of the hero left the timeline. In A Link to the Past, it was apparently because the hero of that era (Hero of Time) failed to defeat Ganon.
Sometimes, the Sages solve the problem as is what happened in A Link to the Past. Other times though, the gods directly intervene as is what happened in Wind Waker.
In Echoes of Wisdom, the Golden Goddesses broke their tradition of silence and directly spoke to Zelda. This makes sense considering the great evil of this game was Null, the direct opposition to the Golden Goddesses and the largest threat on a cosmic scale.
In Twilight Princess, the banishment of the Interlopers itself was a divine act of the gods through the Light Spirits.
I think all of this demonstrates one thing: In the face of a sufficient threat and the absence of a hero, the gods will directly intervene in the world to prevent disaster.
In Refounding, it is a disaster like this that led to this "reset" of Hyrule. Rather than intervene by flooding Hyrule or banishing people to the Twilight Realm, the gods chose to send the Zonai who would have defeated whatever threatened the land of Hyrule and worked with the mortals to stabilize the land to be suitable for life.
There is actually one other time this has potentially happened: The Minish.
We don't know the true origin of the Minish other than that they live in the "Minish Realm", but think about the the nature of the Minish for a moment. They are animal-like humanoid beings from another dimension. They arrived in Hyrule bearing a sacred relic, the Light Force, and used that power to defeat evil (by giving the Light Force and the Picori Blade to the princess and hero) in the War of the Bound Chest. "Who" exactly "sent" the Minish is totally unknown, but it shouldn't be lost on you that the Minish appeared in Hyrule's hour of need and saved the day with the aid of sacred relics.
3. Refounding
This part of the history is why I chose to stick to Refounding over attempting to mix True Founding in as well. I won't get into an argument for Refounding as that is its own line of argumentation, and it's also impossible to solve without additional developer clarification anyway.
I think in a True Founding scenario, there's enough changes to the narrative that this entire line of thinking both just wouldn't work (The Zonai would predate the Twili) and also leaves the Sheikah Eye question unresolved still. The Wild Era Sheikah clearly derived their Sheikah Eye from the Zonai despite the true symbol coming from a much earlier era, leaving the dynamic of the Zonai having a third eye and being the future Sheikah's inspiration to be more of a coincidence.
In a refounding scenario, the Zonai appeared out of nowhere in Hyrule because they did not exist in Hyrule until that point. Like the Minish/Picori, they came from another dimension; for the Zonai, they were returning from their rehabilitation in the Twilight Realm.
4. Additional points
In Twilight Princess, the Mirror of Twilight is broken by Midna which is clearly meant to signify a permanent severence of the Twilight Realm and the World of Light. How could the Twili leave the Twilight Realm if the only key to the realm has been destroyed?
The answer to this may feel like a cop out but it's pretty simple: The gods (Hylia, the Light Spirits, etc) released them. Remember that the entire reason the Twili are in the Twilight Realm is because they were placed there by the Light Spirits. Whether or not the mirror was used to do that is unknown (in the sense that it's unknown if the Mirror of Twilight is a relic given to Hylians by the gods to access the Twilight Realm if needed, or if the Mirror of Twilight was literally used by the Light Spirits as the way they banished the Interlopers), but the fact of the matter is it was the power of the gods that put them there and the power of the gods should be able to release them.
Aside from the issue of the Mirror of Twilight, wouldn't the Twili leaving the Twilight Realm break the intent of Twilight Princess's message, particularly the finale?
This obviously depends on the player. This theory does not suggest Midna herself ever left the Twilight Realm. The proposition here is that the Twili as a collective tribe are slowly being purified by sacred Light, a process that could take untold eons. Their eventual release does not diminish their punishment just as a karmic sentence in Naraka does not diminish the impact of the negative karma. In fact, this sentence should be seen as merciful as corrupted servants of the gods would be worthy of remediation. It is consistent with series lore that the actions of a person don't define that person forever. Whether it's through a spiritual rebirth like Byrne in Spirit Tracks, or a Force-driven transformation like Batreaux, the future of an individual is always open.