The reason for the plot changes is... He's in another dimension! Zelda, Ganon/dorf, didn't wind up in another dimension. Ganon is in the chamber of sages,Zelda is at the castle waiting for Link to return, and Link is trying to save termina while looking for Navi!
"I Don't Love a Girl Because Of Beauty, I Love Her Because She Sings A Song That Only I Understand"- Ducka