Ruto rules the land as a benevolent monarch, using her might for good.

Despite the urges to dominate, to destroy, and cruelly control, Ruto remembered who she was, who she had been. She had been a hero, damnit. And now she was a queen. She had a kingdom to rule. Using her now vast magical powers, she imprisoned Ganondorf behind dozens of wards in the deepest pit she could find, and hoped beyond all else that it would hold. Then the rebuilding began.

It took some time for people to get used to their new ruler, and her mood swings. Sometimes Queen Ruto was melancholy, mourning her life as a man that she had lost forever. Sometimes she was distraught, unable to accept her large, masculine form when all she had wanted since she became a woman was to be feminine, desirable. Sometimes she was as pleased as a cat with a canary, savoring the power and strength she now commanded. Eventually she took a lover, and mothered a dynasty of powerful rulers. The Hylian Royal Family? Never heard from again. Instead, the Sheikah reappeared, and began to protect the new Zoran Royal Family, and Hyrule prospered.

THE END

...or is it?