Howdy, I will be going over a synopsis and slight theory(s) about the history of Calamity Ganon from the Era of the Wilds. I will go over what we know and improvise the missing context between BOTW and TOTK. Let's get to it.
What we already know is that Calamity Ganon is a pure imbodiment of evil, made out of bulging substance called Malice. Returned time and time again, until 10,000 years ago, the Ancient Hero and Ancient Princess sealed him. That's what we were told... however, it is not specific on how it meant. How it was told was unclear, nearly forgotten as a connection to Ganondorf. I will try to make it clearer as much as I can...
The Story
After the Imprisoning War, between centuries of that and after came amok of the Gloom arriving on the surface of Hyrule. The people could have seen a figure, like a phantom of sort from the Demon King. Causing sickness and danger to the land, but disappears for as the seal from Rauru might have been strong to seal the darkness from Ganondorf's stasis body. And each return became widely known for Hyrule's people, and more dangerous. The ancient people sought knowledge to understand what this is and how to stop it. They learn that a male Gerudo once nearly destroyed the world. The people of Gerudo forbid any mention of him, even his name, or it has been so long they nearly forgotten his name or what he used to look like, but they recollected all they can of this man. Speculated to be him again not knowing it was his own evil power taking a conscience. The royal family understood this information, and took action. The Sheikah tribe assisted this phenomenon and first built various towers to indicate and alert Hyrule when Ganon arrives. Inspiring what was the Zonai tech, the sheikah possibly used the same energy that powered the Zonai machines into their own, or extracting Rauru's sealing spiral to power and counter the initial Gloom; creating sheikah Magitech. The royal family then ordered an attack to finally seal Ganon, setting a perimeter, they needed someone to fully seal Ganon similar to the first time. It was a princess who held the blood and power of both from the Goddess and the first King and Queen of Hyrule. She needed someone to protect her, an ancient unknown species of Hyrule that earned the Master Sword and became the knight to protect the princess and weaken Ganon. The sheikah then built the Divine Beasts to assist the Hero with Ganon and made the Guardians to protect him. Unbeknownst yet prepared, Ganon returned and he was more monstrous than before. Taking the form of a boar with arms and serpentine body, this form was vaguely different from the last; it evolved and grew from what was Gloom into now known as Malice. This monstrosity the beast took was affecting the land and its monsters, they gave a new addition to his name: Calamity Ganon. The Sheikah tech alerted all of Hyrule and war ignited. And a one and done battle, the Divine Beasts, Guardians, the ancient champions, the Hero and the Princess did their job and succeeded. Sealed Ganon away, and brought peace for the longest time without sight or worry of the Calamity.
And you know what happens next... so that's what I believe that's what happened. Gloom evolved into Malice, Ganon grew over time, and his origin is blurred from the people Hyrule and had to counter what they already know and succeeded. What do you believe?