As life was beginning to conquer the earth, and animals began to dominate, an odd phenomenon began to occur.
New...beings began to be created. Organization and Destruction were alerted to the creation, and moved to discover what was occurring.
A mother, tending to her young. After some investigation, they discovered that the mother had an ability to eat plants that were toxic to that species previously, and she had transmitted that power to her young. As they watched, an entity known as Transmission began to be formed. Strangely, it seemed to be "he," but neither Organization nor Destruction knew enough about how these things were determined to be too curious. Nevertheless, Transmission was created, in the form of an animal, a butterfly. Puzzling, until they decided the small creatures did transmit the ability to reproduce from plant to plant.
Further investigation revealed that this was not the only instance of Transmission, but it was the focusing aspect of it, apparently the final piece to form the new being, apparently an empowered entity representing that ability to change those around you, as much as Organize and Destroy represented their aspects.
The two decided to raise the young one, to teach him of his abilities and help him do whatever he decided to do.
At the same time, though, they needed a name for themselves. In their language, they called themselves the Existing, though in time they would be known as kwamis. To avoid confusion, however, we will call them kwamis throughout.
They were further interested when another kwami was created, while the first was still young. They found her where a large lizard was attacking a smaller lizard. The smaller lost, but somehow, a kwami was formed, Emotion, the embodiment and, in truth, goddess, of those strange urges the animals felt to run from others, or to mourn the dead.
Another was soon formed, in a similar circumstance where a mother was protecting her young. Thus Protection was formed. Another from small creatures hiding behind plants, leading to the creation of Illusion. The last was formed by large creatures using force to prevent others of its kind from intruding, giving way to Subjection.
By this point, Transmission had begun to use his powers to widespread effect, causing creatures to change over time more than they were before. Creatures became more and more diverse, and as Emotion, Illusion, and Protection became more skilled, they put their own influences on the creatures.
Protection began with thickened skin, bony plates, other things that could defend, but moved on to spikes and other weapons to defend.
Illusion began her influence, affecting animals to disguise themselves, first to make both predator and prey appear to blend with the environment, then to make animals appear larger, or something different from before.
Illusion and Protection worked together for a time, creating small, colorful bugs and fish, that mimicked the appearance of other creatures, distracting predators or scaring them.
Subjection worked on large and small animals, causing some to gather under the banner of the strongest member, while some tiny creatures became dependent on one member of the society for life and responsibility. She also created toxins, allowing some to destroy their prey with a single bite, while others dissuaded potential predators from attack with foul odors or toxic skin. Illusion saw these toxins, and with the help of Protection, began changing some creatures to resemble the toxic ones, so the danger of one would protect the other.
Emotion was content, however, to influence the way members of a species interacted, giving bright colors or special activities to assist in replication of the species. Her favorite, though, were birds where the male had a tale that grew to over three times his size, covered in dazzling spots and colors. All for the sake of attracting a female.
And so it went, and likely would have gone forever, had Destruction not gotten bored.
I hope my headcanon for what kwamis are came through here. If not, here it is in a simpler form.Kwami are abstract creatures given physical appearance, with power to enact their "aspect" as it were. Animals were created by the kwamis, and had some measure of intelligence. Through some mechanism that I never figured out, nor do I care to determine, if a large number of beings develop a concept not covered adequately by existing kwamis, a new one is formed.Also, I have no idea whether the Miraculous in the series were the only ones ever made, but I'm pretending that they are. It makes this all easier.