Remember to equip the Hylian Shield.
Enter the Temple
If you go over to the kid-sized hole you can crawl into, you find a Gerudo woman blocking your way. She asks you what you're up to, but asking about the temple or the Sages will get you nowhere. Say "nothing, really", then say you hate Ganondorf. Nabooru hates him, too, and gives you a task... since she's too big to crawl into the hole, she wants you to go in yourself and find the Silver Gauntlets, and give them back to her when you're done, so she can sneak further into the temple and find Ganondorf's hideout. Agree to it, then get your slingshot ready and crawl through the hole.
Don't go too far in or you'll hit the razor trap. Slingshot the flying keese right away, then get past the trap and up the stairs. There are two more keese on the back wall, so slingshot them. Avoid the spinning trap to awaken the Armos. Kill it with a bomb or bombchu and the two doors will open. Go through the left one.
Carefully kill the Stalfos that drops in, then approach the gap and you will see a green Bubble floating around. Wait for the green flame to go away, and slingshot it. Then you have to hit the switch behind the grate with your boomerang. Face to the left of the switch and throw the boomerang, and it should arc around and hit the switch. You may have to adjust your position and angle until you get it. The grate will fall and you can cross. Avoid getting hit by the flying pots, and open the chest for five rupees. Go through the door.
If you have Din's Fire, approach the middle of the platform and use it to kill the Anubis. If you don't have it, you have to hit the switch and lure the Anubis into the flames. Go through the door.
Don't go too far into the room; a wallmaster is lurking. First kill the keese (there is only one flying around on this side of the fence), then go further in to lure the wallmaster down. Kill it, then target the keese on the other side of the grate and boomerang them to kill them. Collect the silver rupees (one is hiding behind the torch in the corner) to make the bridge fall. Once it is down, cross it and turn around to boomerang the gold skulltula and collect the token. Then light a deku stick with the torch and light the two unlit torches to reveal a chest containing a small key. Get it and leave.
Back in this central room, crawl through the hole between the lanterns and unlock the door. Kill the skulltula on the climbing wall, then get near the wall and face the opposite wall, and slingshot the gold skulltula above, and boomerang its token. Climb up the wall to the next room.
Kill the skulltula on the wall from near where you entered this room. There are two Lizalfos hiding here, so go around the room to make them come down, and kill them. Then use a bombchu on the loose rock in the wall to light the sun switch and open the door. If you have no bombchus, boomerang the crystal switch to make two chests fall, one containing five rupees, the other, some bombchus. Exit this room.
Turn left and push the Armos statue off the edge, and it will land on a switch. Go up the stairs and before going through the door, light a deku stick and jump to the bottom floor, to the center, and light the unlit torches. A chest appears containing the map. Climb up the wall where the Armos fell, and go up the stairs and through the door. In the corridor, simply head through the next door.
Bomb the three beamos so you can move safely around the room, avoiding the traps. Collect the five silver rupees to light the torch. Go around the room, figuring out where the three unlit torches are, then light a Deku Stick and go around lighting the torches. A chest appears, containing a small key. Grab it, then to get to the next room, move the grey blocks around until you can pull the sun block out and into the light streaming in from the window. The door will open, so go through.
In this corner, walk forward, turn around, and kill the gold skulltula above the door for its token. When you're ready (hopefully with at least one fairy in a bottle), go through the locked door to meet your first...
Be VERY careful; a hit from Iron Knuckle costs you four hearts! Turn the corner to see Iron Knuckle, then hit it with your slingshot to wake it up from a distance. Lucky for you, Iron Knuckle is very slow. To hit this mini-boss, carefully walk in front of it while targeting so it will try to chop you with its axe. Quickly side-jump or backflip out of the way, and jump attack Iron Knuckle while it pulls its axe out of the ground. If you run low on hearts, stand behind a column or the throne such that Iron Knuckle will walk to it, where it will chop it down with its axe, releasing three hearts. Eventually, part of Iron Knuckle's armor will come off, letting him move faster. Continue fighting carefully until you defeat it.
Go through the door behind where Iron Knuckle's throne is/was, and go outside. You're on one of the Desert Colossus's hands, where you see a big chest. The annoying owl has a few words to say. Listen, then when it flies away, open the big chest for the Silver Gauntlets.
Suddenly, you hear a scream. Below, two witches are circling Nabooru, who is caught in a magical vortex. She struggles to pull free, but is pulled down into it. The two witches fly into the Desert Colossus.
Guess you can't give Nabooru the Silver Gauntlets, huh? Return to the Temple of Time with the Prelude of Light and pull the Master Sword from the pedestal to become an adult again. You'll automatically be wearing the snazzy Silver Gauntlets. Now you can push around giant blocks! Play the Requiem of Spirit to return to the Desert Colossus.
Before entering the Spirit Temple, turn it to night, go over to the tree by the empty pond, and longshot the gold skulltula in the tree. Now, ride the beanstalk until it flies over a rocky mound (the one on the right if you're facing the Desert Colossus). If it's still night, a gold skulltula will be sitting up here. Kill it for the token. Finally, ride the beanstalk again until it goes over the rock arch in front of the Colossus, and grab the piece of heart there.
Now you're ready to enter the final Temple!