Genesis+To the Beginnings (No BS version)

As the Strongholds faced Ara during the Battle of the Weeping Plains, time ground to a halt and stopped: regular people were not aware of this, but those who would later become known as Constants still experienced time passing, although unable to move. The Incubus Mundi was seemingly unaffected by this event as well, continuing to spill its Ink in the lower Oniric Plane.

There is no canon lore explanation for this event, as it is part of the game's meta narrative.

During this time, having nothing left to observe the Shard of the Maker slowly developed a sense of self: knowing himself for the first time, he decided to gather his strength and allow the Strongholds fulfill their destiny.

He absorbed all of the Ink the Mundi had spilled until now on the bottom of the Oniric Plane, and once that was over he started drinking it directly from it; after a mind-numbing amount of time he rose as The Maker, a new breed of God who could influence reality with yet unseen scope and focus.

Using his newfound powers he rewound the world back at the start of the Strongholds' adventure and allowed them to finish it this time; he couldn't allow them to actually slay the Mundi like they were supposed to (as it was now the source of his powers), but he took great pains to ensure the world would behave exactly like it had been.

And so, an happy ending was reached and the universe trudged on until its eventual end.

At the end of time, however, the Creator wondered if things could have done differently. He rewound time once more back to the Bloodbath (the farthest "safe" spot to rewind to, as that's when the Mundi was created) and started experimenting... And never really stopped, building world after world, thousands and thousands of times, each different from the last.

Although the overwhelming majority of creatures and even some geographical locations are completely unique there are some entities the Maker has no direct control over: these are called the Constants, and though they can be extremely different people depending on the circumstances of their birth and upbringing, they retain a "core" of some sort.

Depending on the individual they might also retain some information of their past lives, although it doesn't usually go past recurring dreams or half-forgotten trivia.

Constants and the Maker are also agnostic to each other: the Maker cannot directly influence or even physically touch them, nor they him.

More information about Constants and Sequiturs can be found on their respective pages.

Eventually, an Ara both knowledgeable and ruthless enough to carry out a plan against the Maker came to pass: exploiting the birth of her children, she made plans to rid them of their identity and Oniric presence, so that they would be overlooked when another reset came to pass.

Then, using the Oniric Arts she had remembered and cultivated for all of her life, she caused a world-ending cataclysm that forced the Maker to trigger it, hijacking it at the last second to add her son and daughter to the mix.

This caused a chain reaction that resulted in the split and incoherent Naluund that we see in the game, the result of a world desperately trying to make sense of itself despite two impossible beings within it.