Ganon is now sealed away along with Zant. Midna has gone back to Twilt after breaking the mirror. She had had a child over the years who had grown up watching over Hyrule through the looking glass in Twilt. As time went Midna also passed on leaving her daughter as the new princess telling her a way to get back to Hyrule if trouble ever happened. Link lived the rest of his life happily and as he died his soul remained.
It has been a thousand years of peace in Hyrule but, now monsters have returned and Link's soul has been born again will he be able to destroy the evil this time around not yet knowing his destiny?