Actually that setting has a lot of potential. Here's a quick example:
The following might be a little inconsistant with previous games,
this is just a brainstorm.
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Evil comes to Hyrule once again. One brave lad answers the call. Travelling
throughout the land, he fights evil, overcomes incredible odds, and navigates
impossible traps. Along the way, he enlists the help of the princess on his
quest to reach the master sword.
Finally, after many trials, the blade is reached, and the lad tries to extract
the master sword. But try as he might, he can't extract the blade. He
apparantly, isn't the hero of legend. In addition to this, the efforts of the false
hero initiates the endless rainfall that will ultimately submerge Hyrule.
Needless to say, Zelda is pissed.
Desperate to undo the damage he has done, the false hero and the princess
search Hyrule for answers. Where is the real hero? Does there truly have to
be only one destined hero per Hyrulian crisis? Should Zelda be concerned that
she is growing interested in a boy who is not a hero of legend?
To make matters worse, the only way to end the rain prematurely is
for Gannon or Zelda to kill the false hero. Will Zelda cave in and kill (or
let Gannon kill) the lad for the good of Hyrule?
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That game could potentially be the darkest game in the series. The fact that we
know Hyrule is doomed from the beginning only serves to make the plot more interesting.