The Master Sword isn't an easy weapon to get hold of as it "chooses" who its wielder will be. Link is the only chosen wielder of the blade. After he was trapped in the Dark Realm, Link combined his spirit to Mario's so that he was able to use the Master Sword himself to defeat Ganon.
It was first unsheathed in "And then there was Nox Decious" and wasn't seen again until "Like Hyrule, but not" (it wasn't used for that long due to an accident on set). Link uses this sword to deliver the final blow to Steven Bauer in the episode "Blood Money."
In the original Legend of Zelda games, the Master Sword was originally called the Goddess Sword and was the created by the Goddesses of Hyrule.