They prayed the gods, only or no one to receive their prayers, no hero was sent.
It would be first and foremost, probably the darkest Zelda game ever. Darkness doesn’t necessary mean what people think, but at the same time look at the imagery from Wind Waker. Inside the Temple of Time under the water lies a castle stricken by enemies swarming in from all sides frozen in the depths of time. If a game was to be ever set in the Great Flood period, it would be one where the protagonist fails, and one which a kingdom fails.
If this was on IGN, this article would be called “What Zelda could learn from GTA”. For the following gameplay suggestion. While GTA V was overly just the GTA formula a little bit more fleshed out, thus providing a more indulging experience. The game also introduced a mechanic to the series which involved switching between other characters, instead of just playing as one protagonist. I propose this would be perfect in a Zelda set within the flood.
Think of it, another reason why this Zelda game would be so dark, is because of its powerful connection to religion and its impracticality which is pushed onto its lands because of it. As well as comparison to real religion by many. In the era, all the tribes and sectors of the Hyrule community pray to their gods only to have no reply until it is too late, when the goal is lost and there is no chance to rebuild within their own lands. Forced to the mountain tops in a “hey guys, we are here, wow you really screwed up, don’t worry we will flood the place”, it isn’t hard to imagine that these tribes fed up prior to this would have sent their very best heroes out to try and save the world themselves, after ages of praying with no answer from their gods.
If you look back for a moment in Ocarina of Time, as Link did his world tour, he went to many tribes and communities in the Hyrule Kingdom which had already started sectoring out and showing that they have the strength and ability to combat the evil which Link ultimately sorted out. It isn’t hard to imagine that the Hyrule in this proposed game would be one of segregation as well, and one which each tribe had sent their best to combat the evil.
So this of course would be those who you would play as, in the GTA style switching gameplay. A member of each tribe. Which you will learn about their trials and tribulations during a time with no hero, as they battle through the land almost succeeding, but pushed back by evil due to the lack to seal away the evil for good and the Gods horrible timing and solution.
In general the gameplay would be about the same, but the world is riddled in evil so monsters would be everywhere. It would be what fans saw “awesome” in the Twilight Princess reveal trailer. The climactic battle scenes and the feeling that there is a fight for the death happening not that you are the hero, you will win.
If there is ever a time, which the flood resides and those come down the mountains again. What will be seen is a world which the temples of old are neglected, and the religion of old lost due to a grudge of the past which the tribes would never forgive the Gods for.
Those wanting their sequel to Majoras Mask in terms of gameplay, should be asking for a Great Flood game instead. The moon, replaced by the impending waves. Instead of time traveling to avoid the inevitable, you face up to the challenge but fail. A lesson in the game that even normal people can rise up and be heroes, but the challenges faced can be crippled by those you thought held your desires most close.