As in the original game, the Spirit Temple is reached by crossing the Haunted Wasteland and learning the Requiem of Spirit from Sheik in the Desert Colossus.
Play the Requiem of Spirit and warp to the Desert Colossus. Now go into the Spirit Temple.
In the entrance room, the treasure chest that you'll find contains Bombchus. On the other side of the wall, there's a crystal switch that when hit, makes another chest full of Bombchus drop down. Now, use a regular bomb to destroy the rock behind the snake statue, then hit the eye switch to make a third chest drop down, which contains a Small Key.
Talk to Nabooru and say that you are doing nothing. She will then ask you to find the Silver Gauntlets. Crawl through the hole she was standing in front of. On the other side, you'll find a bunch of torch slugs, which are super dangerous because your Kokiri Sword won't even put a dent into these things. You need to jump attack them if you want to hurt them. Once they're gone, the two doors will open. (Hitting the eye switch, by the way, turns off the fire guarding the Recovery Hearts.)
Go through the right door and first of all get rid of the Gibdo you see. Pull back the right grave to reveal a switch that will open the grating. Pull out a Bombchu and place it so it will travel through the open grating and destroy the rock on the other side. This will reveal an eye switch that, when hit, makes a platform appear allowing you to jump across. Destroy the two Gibdos on the other side as well to make the door to the next room open.
You'll come across a large spinning platform. Jump on it and a Stalfos will appear. Either kill it the regular way, or knock it down the bottomless pit to make the fire disappear and the doors open. In the next room, get rid of the Keese, then pull back the grave to reveal a switch that will make the grating fall down to form a bridge. Cross it and open the chest on the other side to get the Dungeon Map. Kill the Anubis with Din's Fire and once all the enemies are gone, a treasure chest containing another Small Key will appear. Go through the door to return to the Torch Slug room.
If you try to crawl through the hole, you'll notice it's blocked by a rock. Use a Bombchu to destroy the rock and you can crawl through. Go through the locked door. Here, you'll face great danger - a Like-Like is above you, and as soon as you hit the crystal switch to open the gate, it will drop down on you. If you have Din's Fire, you can simply use it to kill the Like-Like (it will not trigger the crystal switch), otherwise be prepared for a fight. Once this is done, climb up the wall.
Kill the Beamos and the two Baby Dodongos here to make a chest with more Bombchus appear. Target the boulder at the wall and use a Bombchu to destroy it, which will make a treasure chest appear - except you cannot reach it, so go through the locked door. Jump down and shoot the eye switch at the left side of the statue, then go to the treasure chest in front of the statue (watch out for the Wallmaster) to get the Compass. Turn around and unfreeze the frozen eye switch with Din's Fire, then go through.
This room may seem like a dead end, but look down the pit and you'll discover an eye switch. Hit it and open the treasure chest that appear to obtain a Small Key. Go back through the door, climb up the wall to the left (where you originally came from) and go upstairs. Go to the right and look down the pit to notice a blue block with a crate on it. Jump down onto the blue block, pick up the crate, turn toward the wall and play the Song of Time. Another blue block will appear, making it easy to jump back to where you were (you can also skip the second block and jump straight over the railing, but it's trickier). Walk back upstairs holding the crate. Once back up, play the Song of Time to make the blue block move up, allowing you to jump across with your crate. From here jump onto the statue's right hand (i. e. your left) and drop the crate to open the door at the top, allowing you to go through.
In the passageway run across while the flamethrower's inactive. Go through the door to enter a small puzzle. Hit the crystal switch with the slingshot to make the flames go out. Go to the other side to find two blocks with sun faces next to each other. Pull the back block into the light to make the doors open. (The other one makes a chest containing a Recovery Heart appear. Don't push any of the other blocks into the light.) Shoot the crystal switch again and get across. Here, kill the Skulltula and then continue.
You'll now have to face an Iron Knuckle. The first thing you should know is that its axe hurts a lot, so avoid it at all costs. The easiest way to get rid of him is making him use his axe, then jump attacking him and getting back again. Alternatively, you can simply lob your bombs at him. If you need some health, let the Iron Knuckle destroy the pillars for some refills. Once he is killed, the door behind him will open. Go through and once outside, open the chest to get the Silver Gauntlets! You'll then see Nabooru getting abducted...
Return here as an adult to do the second part.
The water jet to the east is absolutely impassable. Instead, look up at the ceiling to notice a rock. Use a well-placed Bombchu to hit the rock which reveals a Longshot target, then pull yourself up. Use the Silver Gauntlets to push the block forward into the pit, then go through the door to arrive in the statue room.
Climb up the west wall and go through the door to return to the room with the unreachable chest. With the Longshot, you can now reach it to get a Small Key. Hit the crystal switch, then jump down the passageway and go through the door here. Hit the rusted switch with the Megaton Hammer to make a treasure chest appear. Return to the room with the statue and this time go up the stairs. On the other side you'll see a Floormaster as well as a torch. First kill the Floormaster with your bow, then use the Longshot on the torch to get across. Go upstairs and enter the locked door.
Use your Longshot and pull yourself to the Hookshot target on the ceiling to get through the passage unscathed. In the next room, kill all four Beamos here to make a chest appear (it contains just arrows, though). Play the Song of Time next to the blue block on the ground and it will appear on the other side of the room. Go across and play the Song of Time twice (yes you read that right). This will make a small crate appear, which you should drop on the switch at the other side of the room to make the door open. Go through to the next area.
First of all tackle the two Dinofols that appear here. Opening the chest you see just freezes you in a block of ice, but slash it with your sword and the door to the next area will open. Here, you'll have to fight an invisible Floormaster - use the Lens of Truth and shoot arrows at it, then turn off the Lens and use Din's Fire to get rid of the small hands, this will make the door ahead open. In here, you'll have to fight another Iron Knuckle. Thanks to your better sword, he's easier than he was as a child, so duke it out with him, then go through the door. Outside, open the chest to obtain the Mirror Shield.
Get back to the Dinofols room. Jump onto the blue block and use your Mirror Shield to reflect light onto the sun face, this will make the other door open. A Gibdo awaits you on the other side, so immediately pull out your Ocarina and play the Sun's Song, then slash him. Open the chest he was guarding to get the Big Key. Return to the statue room.
Here, there are three torches that need to be lit - two to the sides of the statue, and one in front. It's hard to find a position where you have a clear shot at all three - the best one may be the blue block with the crate on it. Use Fire Arrows to light all three torches, which will make the lower door on the east side open. Use your Longshot to get across and go through.
This room is extremely dangerous. You have two Stalfos, and a Wallmaster to make it ever the more annoying, and you actually have to destroy it. Once these are gone, try to light the sun faces... except it doesn't seem to work, instead simply exit and reenter the room. The Stalfos and Wallmaster will be back, but the sun faces won't, so kill them again to open the grating. Jump down and go through the door.
Collect the Silver Rupee next to the door. Walk down to the water jet and turn around to find the second Silver Rupee. Destroy the boulder and hit the rusted switch with the Megaton Hammer to turn off the water jet, quickly run across to grab the third Silver Rupee. Back in the main room, destroy the two boulders beside the snake statues to find the other two Silver Rupees. Open the chest that appears for a Small Key.
Return all the way to the room where all the Beamos were. Open the locked door on the other side. First of all, kill all the Fire Keese above you. You'll notice the wall here is full of Silver Rupees. Use your Longshot on the top segment that doesn't move and you should be able to get all of them just by falling down. Afterwards, Longshot the highest segment again and climb up, watching the Torch Slug that patrols up there, and go through the now open door.
Play Zelda's Lullaby on the Triforce symbol to open the next door. Here, drop down and destroy the crates until you come across a rusted switch, hit it with the Megaton Hammer to make the next door open. Go through and kill all the enemies you find here. Use your Mirror Shield to deflect light onto the sun face, which will cause the fire further down to go out for a while. Run down to the end and push the snake statue so the mirror faces the bars. Now return to the other snake statue and rotate it so the light is reflected all across the passage to the end.
Now go back to the previous room and jump down. Reflect the light onto the sun face and the entire platform will move downward. Immediately watch out for the Wallmaster trying to grab you - you should kill it to give you an easier time. Deflect the light onto the statue's face to make it crumble, then use the Longshot at the gate to pull you to it. It will automatically open to let you through, so open the boss door...
Mini-boss: Nabooru (Brainwashed)
Nabooru has been brainwashed to be an Iron Knuckle. This fight isn't much different from the previous two. If you want, you can simply drop your remaining Bombchus here, since they won't be of much use ahead in your quest. After enough hits, the Iron Knuckle's armor will fall off to reveal Nabooru, however she is quickly captured. Go ahead through the door and climb the platform to fight the boss...
This fight isn't any different from regular Ocarina of Time. In the first part, use your Mirror Shield to deflect one witch's magic onto the other. After enough hits, they'll join to form Twinrova. Now, use your Mirror Shield to capture three of the same spell, then hit her with it as the shield releases its stored power and get a few hits on with your sword. Repeat this procedure until she's dead.