NOTE: based off this image: r/zelda/comments/730jvm/breath_of_the_wind_flooded_hyrule_concept_map/?utm_content=comments&utm_medium=hot&utm_source=reddit&utm_name=zelda
Prologue - A Second Calamity
It all happened so fast. Link swore he was going to go to Zora's Domain next to help with Vah Ruta. But he got distracted, forgot what he was supposed to be doing. And now it's too late to fix his mistake.
When he saw the Red-Maned Lynel on Ploymous Mountain, Link realized that he couldn't possibly take it down. Self-preservation kicked in, and he fled, promising himself that he'd come back when he was stronger, when he didn't have to fear the Lynel.
Now, by Ralis Pond, watching the water gush across the land below, the guilt overwhelmed him. He'd been tasked with saving Hyrule, and he'd failed. He had let Zelda down, he had let the king down, and he had let all of Hyrule down. Then another pang of guilt. He'd let the other Champions down too. Urbosa, Daruk, Revali, and Mipha - he'd let them all down.
The water showed no signs of stopping, either. Vah Ruta's wrath - or perhaps it was panic - continued, slowly engulfing more and more of Hyrule. For a few moments, Link was mesmerized by the swirling waters, bringing him some momentary peace. His mind, in its calmed state, wandered and briefly reminisced. He subconsciously closed his eyes, the sound of the water almost soothing him.
Until he was jolted awake by the feeling of water at his feet, at his ankles, soaking into his leggings. With horror, he realized that his momentary lapse in concentration had allowed the water to come closer. He scrambled to get to his feet, for fear that the water's sheer speed would pull him under once it got deep enough. But as his rotten luck would have it, he'd chosen to sit on the wrong side of Ralis Pond. A mad dash towards the nearest piece of land proved futile, as by the time he'd gotten there the water was up to his waist. Link strained against the current, but it proved too strong and whisked him away, towards where the Lanayru Tower once stood.
Link's body wasn't found until several weeks later, washing up on the shores nearby where Kakariko once was. The ones who found him didn't recognize him - not by name, anyways. They knew him as the kind young man who'd saved them from monsters once or twice. They honored him as best they could, with a sombre burial on what came to be known as "Pierre Island". The grave had no name, as they'd never heard him speak it, so it was simply marked "Our Silent Protector, may his spirit find rest in the afterlife."
Hyrule was once again without a Hero.