The Master Sword is locked away in the basement of Hyrule Castle, keeping Ganon's army frozen in time. After Link solves a minor block puzzle, he gains access to the basement and can withdraw the Master Sword from its pedestal. This causes all of the frozen enemies upstairs to being moving.
When you first get the Master Sword, it isn't at full strength, as the power to repel evil has faded. Once Link reawakens the Earth and Wind Sage, its power is fuly restored and he can gain access to Ganon's Tower. The Master Sword is generally stronger than the Hero's Sword, although some enemies still take the same number of hits.
