With the three pendants in hand, you now hold the keys to removing the Master Sword from its pedestal, deep within the Lost Woods. Let's go!
Head west from the Tower of Hera, past Spectacle Rock, to a ledge where you can fall down. Once below, head to where the ladder is. For a quick way down, walk up against the ledge to the left of the ladder, and you will fall down to the base of the ladder (you won't get hurt). Go through the door here, into another dark cavern.
The path here is straightforward, so just go through until you reach a door. Go through it, and dash attack against the left wall and you will head down towards the door, but stop dashing after a while or you will hit a wall and fall into a hole! Go through the door to the outside.
Drop down the ledge here, then exit to the screen to the north. Pass by the lumberjacks, and enter the Lost Woods via the northwest exit.
-- Lost Woods --
In the cool, misty Lost Woods, there are many imitation Master Swords in tiny pedestals. Just ignore them (Link is fooled by them, apparently... even after he gets the real Master Sword). Head west, avoiding a crow that flies at you. When the path turns south, head south through a log. From there turn around to the north (going through the other log if you want), and head west to where you should have collected the magic mushroom (if not, get it now). Go up through the log here. Continue on until the path splits. There will be a log to the south and a log to the northwest; take the northwest one.
You reach a clearing in which many squirrels and birds are playing peacefully. The Master Sword beckons from above; go north towards the sacred blade. Soon, through the mist, the pedestal of the Master Sword becomes apparent. There it is; the Blade of Evil's Bane! Ancient words are inscribed on the pedestal; the Book of Mudora deciphers the poem:
The Hero's triumph on Cataclysm's Eve Wins three symbols of virtue. The Master Sword he will then retrieve, Keeping the Knight's line true.
You, the Hero, descendant of the Knights of Hyrule, have won the three pendants; the Master Sword is your destiny. Walk onto the pedestal and stand above the blade, and press A. The three magical pendants will float up and glow with a brilliant light. The Master Sword gleams as you remove it. You hold it aloft, shining; finally, the blade is yours!
The enchanted mist that filled the forest dissolves instantly. Sahasrahla contacts you telepathically, sensing that you now possess the legendary blade.
It is time. Leave the clearing, and suddenly Zelda contacts you telepathically. The soldiers have broken into the Sanctuary! They are capturing Zelda!
If you go to the Sanctuary, the priest tells you with his dying words that Zelda has been taken to the castle. Go there.