Link is riding Epona in a dark forest. But all of a sudden, a Skull Kid knocks Link unconcious and steals Link's Ocarina. Link awakes and sees the Skull Kid with his Ocarina and tries to get it back, but alas the Skull Kid steals trusty steed: Epona [FYI: "Epona" is the Goddess of Horses in Norse Mythology] and goes in a sort of wormhole to another dimension. Link, being the Hero he is follows him into a very familiar land named: Termina. [The alternate Hyrule] But something more happens. Link is turned into a Deku Scrub! He soon finds out this world is doomed for destruction. The moon is quickly falling and will wipe out all the inhabitants. Link [Again saving masses of people] then begins his journey. He is told to stop this cataclysmic event he must find the masked one [Majora obviously] and stop his evil plans. Link searches for The Skull Kid, and on the third day finds him on top of the clock tower (In clocktown). The Moon is near, and Link faces Skull Kid.When the moon is just about to fall to the land, Link remembers the Song of Time and plays it, whisping him back to the first day he arrived.And so the story goes on...

[It's said that Majora's Mask had taken over the Stalkids' body and made him do all these terrible things]