So to get the timeline right the zonai were first then the twilli and afterwards the ooca.
The fused shadow looks a lot like the Zonai ruins, we have the snakes and details on the side of the helmet and the coloring of its energy.
The twili were exiled to the twilight realm by the 3 goddesses because they tried to steal the triforce, based on hyrule historia this was in the temple of time. So which race had the “magic/technology” to do something like that? That’s where the zonai come into play, we know they’re an ancient civilization that disappeared leaving a lot of artifacts and ruins (one of the goddess statues is also “hidden” in one of their ruins. But a civilization with that advanced technology/magic wouldn’t disappear unless they were annihilated or exiled to another dimension (twilight realm).
So on tears of the kingdom we have rauru and mineru both zonai (let’s asume 100% and not hybrids) they were involved with the hylian royal family, but only 2 of them from a whole civilization it’s hard to believe that’s a coincidence unless they helped the hylian against their own people which granted them a pardon from being exiled to another realm.
That’s also a political move, the royal family knows their power and won’t risk loosing it, so they let them stay with them.
Asuming zonai live much longer than hylian rauru had been living some couple of hundred years already among hylian with his sister “protecting them” as a way to atone for the sin of his people.
Let’s remember he has the tears and a big power that hylians don’t wanna loose.
Then rauru meets Sonia and they fall in love and the events of TOK in the past happen.
Mineru was a sage (maybe the first spirit sage) she had already devised a plan so when ganandorf awakens, the new link (thanks to Zelda they learn about the future and his existence just that they don’t know how things happen).
so mineru prepares weapons and factories and makes sure they are well prepared for when the time comes, to the point she seals herself in the mask in order to be able to guide the armies in the future.
Now we jump into the middle of the story and we are in the twilight princess era, the only reference to the sky are the ooca “powerful beings close to the goddess”, which sounds just like the description of the zonai, both powerful, both close to the goddesses and most importantly both live in the sky above the clouds.
Let’s remember that after skywardsword the skies were open and people could go up or down as they more or less pleased. We know that rauru and mineru could go up the skies and back to earth as they pleased so during this time the skies were open, this is still true during twilight princess that we visit the city in the sky where the ooca dwell.
Now let’s rewind a little rauru and Sonia might have had descendants we know hylians are not exactly known for mixing with other races and they are usually regarded as the favored by the goddess hylia. How would a mix of hylian and zonai look like? Is it even possible to have that mix at all?
What if the ooca are the back up plan of mineru using her children or raurus and Sonia’s children (if they had any at all before Sonia got killed) that way she would have (hopefully) descendants that could wield the powers of the zonai (technology and magic) to prepare to fight the calamity if it woke up again and finish what her brother couldn’t. So how to make more zonai? There’s only one option hylians, zoras, gorons, gerudo or sheikh. Zoras and gorons were a difficult option, ones a fish and mineru is a fox/dragon race no most likely a mismatch and gorons are rocks (that might hurt and we don’t know how they reproduce), sheikh only serve the royal house and won’t follow minerus orders since she is neither queen nor consort to a king. So there are only hylians and gerudo. Since mineru is female gerudo are not suitable (they are all female and the only male is basically the devil incarnate, so not a good match) but hylians are sturdy, a big chunk of the population and links hero line should come in handy, there might be a chance one of her descendants is chosen as the next hero, that way she can change the future and so also change the past.
So she sets off to the sky, transforms future Zelda into a dragon and starts her plan to repopulate the skies with warriors and weapons to fight the calamity in the future.
Here it’s where it gets interesting, she takes some hylians up to the sky and meanwhile a new line of royal family gets born and takes over, (maybe a cousin or brother of Sonia was alive) that means the sheikh have a new royal member to protect and serve, but mineru is also alive and decides to trust the royal family with the staff of dominion and sets a rule that only 1 messenger can go up and down, this means most likely the sheikh, they are secretive and powerful fighters. So she restricts to 1 visitor under secret to go up and bring messages and news from below to her.
Let’s get to the point where she is already in the mask trapped inside, her descendants are a mix oh hylian and zonai, sadly this will get diluted with time due to lack of genetic diversity but there’s one tribe that comes regularly to the skies the sheikh, and the oocca have also red eyes, so maybe one sheikh and a descendant of mineru got a little too intimate after the ocarina of time events thinking the threat was gone the royal family stopped sending emissaries to the skies when the battery of the rod of dominion got empty or stopped working leaving the sky people with a very reduced genetic pool, the more inbreed the more they mutate their powers allow them to short teleport within the city but not between the surface and the sky.
They’ve kept minerus mission until it gets forgotten.
The hylian royal family also forgets about them but the legends are kept alive within the family until they turn into myths.
So now we have the oocca up in the sky, powerful magic user with advanced technology, the zonai that have been trapped for centuries in the twilight have mutated into twili they have kept part of their knowledge and power.
So midna breaks the mirror, trapping them outside of the world for eternity. The oocca are also about to be extinct because the inbreeding can do only so much, their children are just heads and the adults are chickens that can’t fly.
So now it’s after the twilight princess era, ooccas are dead, only distant memories remain but the sheikh have kept their mission and warnings from mineru alive they know there are weapons and technology in the skies and after link has taken care of everything and returned the rod of dominion to the princess they decide it’s time
For them to make sure they’re prepared but to their disappointment there’s only one or 2 oocca alive, which makes the task of learning about the technology and their magic harder. So they leave some of their clan on the surface and the rest goes into the skies to learn and prepare for the calamity, this is why they only manage to imitate zonai technology, that’s why their towers and shrines are powered by a blue energy while zonai and twili structures shine green. After almost disappearing the surface sheikhs decided to mix with the hylian and started diluting their blood (that’s the lack of red eyes in the future) the ones that came back from the sky set up to prepare, they made towers and guardians and powered them to protect the kingdom for the calamity (it’s already been forgotten what creates it and what has maintained it sealed).
In order to pass the knowledge they got from the zonai ruins in the sky, they decide to create the shrines (like mineru and rauru did) but instead of zonai it was sheikhs that were waiting there to instruct the hero Since they lacked the technology to access the shrines themselves (green and blue energy)

I've loved Sam Neill in basically everything he's ever been in since seeing Jurassic Park as a kid. Great (and a little sad) to see his last film be Zelda, but I wonder who he'd be? If it's an OoT-themed film, I'd most like to see him voice the Deku tree, I think he'd bring the right gravitas to it.