First, there were normal humans, a race that developed normally through evolution. They became so advanced that they wanted to ascend. They ascended into a single united being - the Veiled woman.
She, however, felt alone and so she created new generation. Those were not as advanced, as her race was, and when she artificially ascended them, they didn't become so powerful as she is but only the High One (thus, she thinks of herself as being something above them and being able to manipulate the real world on physical level, unlike the High Ones).
She wanted to stop the High One, but he wanted to continue and create more and more. They influenced the people on Vyn into doing, what they and the Veiled woman thought was destroying the High Ones through the Beacon, but in reality, the High Ones had everything prepared.
At our generation the power of the High Ones is so great that the Veiled woman can't stop them (and doesn't want to accept their superior power). The only generation that we know of, where the Veiled woman forced the High Ones back, was the Starling generation. They developed so well that they escaped into the stars protected by a barrier that stopped the Beacon's Light.
There also is the Goliath - the person inside it might be a puppet of the High Ones too. In every Cycle, he tells the Prophet about his/her universality and to flee into the Star City. Every Prophet does so, only to become the Aged Man. The Aged man/woman will then wait in the Star City with thier lover, who will get worse over time (becouse of hunger, thirst, etc.) anc they will come back. They will create the mannor. As the Prophet is traumatized by the Cleansing, he makes sculptures forming statues of those in the Light of the Beacon. Even the Aged Man himself said, that he is "an observer. A FLESHLESS eye..." That might imply theory that he is the flessless prophet. After that, the Aged man will give the Word of the dead to the new Prophet to keep the Cycles going.
In our generaion the Aged man's book lock combination was PRIDE WAS MY FALL stating actually what made Tealor fail. The woman in the water would be the Prophet's companion. She even asks the player (mistaking him for Gajus) if "they are there yet" which could mean, that they are returning to the Star City to maybe perform Apotheosis on her.
Maybe this Cycle IS different however. If you choose not to flee to the Star City but to sacrifice yourself (which blows up the whole of Enderal) you actually make a difference and maybe that will change the things in the future (becouse recreating an entire continent would be impossible for the High Ones to keep things same).
That sums up my theory. If you find any plothole in it or something not corresponding with the game's story, just let me know
I would also like to thank SureAI for making Enderal real. This game was an amazing experience. I have never played a game that took me into it so deeply and truly. I have to admit, during the credits, I cried
EDIT: I connected some more dots:
At the occasion with Adilia, the Veiled woman says "I don't want to be seen as a destroyer." That would imply that she is trying to be seen as the good one, and who is trying to be seen as the good one? The one that made a mistake. Her mistake was creating the High Ones, teaching them the Cleansing in the process and not being able to stop them anymore.
You see, there has been the zeroth generation - the Veiled woman's. Then there was the first one - the bear High One. He is symbolized as a bear becouse bears are strong and can withstand a lot. This High One withstood a lot of pressure from the Veiled woman. Then there was the second generation - the wolf High One. Wolfs are known for making groups in which they help each other out. This High One united with the bear High One, and their united power was enough to defend against the attacks of the Veiled woman. The fighting took place during the third generation - the Starling. They managed to avoid the effects of the High Ones, reach the skies and avoid lighting the Beacon. Then, the fourth generation started - the Pyreans. The High Ones were powerful enough now, that they managed to defend against the Veiled woman. The Pyreans failed the fight and became the spider High One. Why spider? Becouse spiders are patient as they weave the strings of their webs. The High Ones know now, that the three of them can defend against the Veiled woman without a problem and so they focus on creating more powerful High Ones to actually destroy her. Durning our generation - the fith one - the Veiled woman understands that the Starlings are her hope. They could evolve to a level that her generation once was at and could help her in the fight. The High Ones understand that as well. They inflict the Red Madness onto the Starlings, who then fight with each other and kill each other (we know that the Light of the Beacon can't reach all the way up there, but the Red Madness can, as Kumai showed us. To let the Star City be grown through with flora wouldn't take long, birds bring seeds and dirt etc. and after a few hundrets of years you have the current Star City). Now the last hope would be our generation for the Veiled woman. She makes the Prophet be a flessless one. If he chooses either of the companions they will always be there for the fight with the Goliath and so the Prophet will survive. And if the Prophet chooses either of the endings, it will be ensured, that they will make a difference (Star City --> Aged man and a new chance for her, destruction of Enderal --> the right way how to fight the High Ones).
EDIT: So, which ending is the canon? I believe it is the sacrifice. If you decide to sacrifice yourself and make the Beacon explode, maybe not the whole Enderal will be destroyed. Ark will surely be blown away, most of Enderal too. Dunevill will be burried beneath the sea. Silvergrove might make it, since the mountain can absorb a lot of the shockwave. Maybe the Aged man's mannor is far away. Maybe the Living temple is far enough as well. Yes, I do mention it on purpose, becouse where is the real you? That's right - right inside the Temple. If you were to play the game from start, at the beginning when you are thrown into the water with Sirius, you hear some voices, mostly hard to distinguish. But if you play this vision the second time, you can actually recognize a lot of them. The last one is Tealor screaming "You fool!" (after Sha'rim's betreyal) I believe. After you decide to sacrifice yourself, your part dies. Maybe it gives your body some fuel. Of course we can't know that, becouse there has never been a Fleshless that has died, untill now. And we know, that your body is there, laying on the ground. So if the same would happen to Arantheal and Coarek, they would maybe wake up in a grave or tomb? Not long untill they suffocate or die of starvation or as an awoken Lost one, but you can actually do something. You have all the memories of being prophet and we still have Veiled donna ex machina on our side.