Final Preparations:

After the story sequence you're back at the Desert Colossus.  Use the Prelude of Light to go to the Temple of Time.  Another, very informative story sequence follows in which you get the Light Arrows.  Now, go around Hyrule and finish up all your unfinished business.  Get all the remaining heart container pieces, complete the trading sequences, kill gold skulltulas you've missed, catch all the 10 Big Poes, catch a huge fish, and try all the cool tricks in the Tips, Tricks, and Secrets section below.  Get everything you can out of this awesome game, because the next step is the final level, Gannon's Castle.  When you're ready, make sure you have at least 1 blue potion (found in the weird potion shop behind the regular potion shop in Kakariko Village) and some faeries and head to Gannon's Castle.  Walk up the steps and a bridge will be formed for you.  Head into the castle

Gannon's Castle:

Walk down the hall, past the two eye laser things (just run past them) and through the door.  Now turn right and follow the outside wall until you find the door with the purple Shadow Temple emblem above it (look on your Quest Status subscreen if you need to compare).  Go through that door, look to your left for a platform with a small chest on it.  Hookshot to it.  Put on your Hover Boots.  Now aim across the way at a small platform with a torch on it, and use a Fire Arrow to light the torch.  Quickly run across the blocks that appear, past the shield-eater and on to the next platform after it.  You won't have time to make it to the next block so don't try.  Instead, use your Lens to see an invisible walkway.  Take the right-hand walk way and jump down to the platform with the switch on it.  Step on the switch to make a big treasure box appear.  Use your hookshot on the treasure box to get up to it and you'll get the Gold Gauntlets.  Now take the left invisible path to a switch.  Hit it with your hammer, then go back and take the right path again to the door.  Go through it and shoot the floating ball thing with a Light arrow.  You'll be transported back to the main room.  Go back to the main door you came in through and leave the castle.  When you are outside go across the bridge and loop around to your left.  You'll run under a stone arch and go down a passageway to a huge stone pillar.  Pick it up using your A button and go through the cave behind it.  Use Zelda's Lullaby to summon the fairy and get double defense.  Now head back into the castle and into the main room.

Now that you have the Golden Gauntlets it doesn't matter what order you get rid of the barriers.  So just head right and go through the first door, the one with the green emblem (Forest Barrier).  Kill the wolf, then use Din's Fire to light all the torches.  Look above the doorway and there's another torch, so light it with a Fire Arrow and go through the door.  Make sure you have your Hover Boots equipped in this next room.  First, wait until the fan to your left is going and then walk toward it to get the silver rupee, then turn right and the fan will help blow you across to the next platform.