Allow me to explain the timeline that this story follows:

After Link defeated Gannon Zelda sent Link back in time, creating another timeline. The first timeline is where the beginning of Ocarina of Time is, when Link collects the spiritual stones. He is sent just before he draws the Master Sword so Zelda did flee form the castle but as Ganondorf dissapeared nothing else happened. After this Majora's Mask happens. This happens when Link is eleven, two years after he came back. After being away from Hyrule for a month, he returns but didn't find Navy the Fairy.

Link remembers all about collecting the Medallions but for Zelda and the rest of the sages and people that never happened.

The King was very impressed with Link's deeds (collecting the spiritual stones and saving Terminia) so they become friends too.

The other timeline is in which Link collected the medallions and Hyrule was partially destroyed.

This story follow the first timeline, The Majora's Mask timeline.

I hope you understood all of what I said. On with the story. Please tell me if you find any mistakes and I'll try to correct them.