The Master Sword is fairly easy to find. Enter the Lost Woods from the path in the northwest corner of Kakariko Village. In the woods, watch out for the thieves that will rob you, and don't be fooled by the fake swords. Head in a northwest direction through the logs and you should reach the clearing where the sword is. If you have all three pendants, you can just approach the sword and take it.
Once you get the sword, you'll soon hear Zelda's cry that the guards are after her again. Return to the Sanctuary and the Priest will tell you what happened. You must now return to the castle to face Agahnim, but you should first return to the witch's hut for more medicine if needed.
Unlike the first time, you can enter the castle through the front gate. In the front room, take the door to the left that's on the same level as the staircase. Head south to get to the door out onto the castle roof. To the right of the door is another door blocked by a power field. Destroy the barrier with the Master Sword and enter the door.
In the second room you must defeat the mace guards to open the door. If all your hearts are full this will be easier as the Master Sword will shoot beams (although they only do half the damage of the blade). Defeat the charging guards in the next room to get the key for the next door. Be careful on the third floor as it is dark.
The second room there is a maze, but there are torches you can light to make it easier. Get the key in the chest on the far left end of the room, then use it on the door at the lower right end. Stay in the doorway when you first enter the next room and take out the charging guards as they come to you before going to the stairs.
On the fourth floor, light the torches in the pit room to help find your way northward. The torches will also help in the next room against the guards you must defeat for the key. The fifth floor is pretty simple until you reach the room with the blocks and pots. The red guard has the key for the door and it takes two pots to defeat him. (There's also a lot of treasure under the pots).
When you climb the stairs to the sixth floor, it may seem like you're blocked by statues, but the one on the far left can be pushed away. Use extreme care walking along the thin path to the next stairway. On the seventh floor you'll find Agahnim - just as he sacrifices Zelda. He will then disappear behind the curtains in the back. Cut through the curtains and follow him.
Agahnim can only be defeated by his own magic spells. When he sends out a fireball, strike it with the Master Sword to reflect it back at him. His ice spells can be deflected with the sword, but not reflected. Lightning spells cannot be stopped and are only used when he teleports to the very back of the room, so run to a corner when he moves there to avoid the lightning. If you hit him with six fireballs, Agahnim will go down. As you'll see, however, the game is far from over...
