With all three Goddess Pearls, you have the keys to a new location. Travel to the each of the Triangle islands and face each of the three statues. They will ask you to place the pearls in their hands. When all three are placed, the statues change shape into Din, Farore, and Nayru, exploding out of their rock shapes, and Link happens to get caught in the middle of an explosion (Poor Link gets too close to a statue and goes flying!)
With all three statues activated, beams of light shoot from each of the pearls and connect to form a large triangle, where the image of the Triforce suddenly appears and breaks the seal in the middle of the islands. Then, in golden flash of light, a collosal tower raises out from the sea (which Link crashes into). After recovering from the staute explosion, Link is greeted by The King of Red Lions. He explains that this is a tower used by the Gods to test the courage of potential heroes.
With the trials of the tower awaiting you, sail on in and see if you are meant to be a true hero.
The Tower of the Gods
Upon entering the great Tower of the Gods, the innerworkings are very majestic, and the first floor is flooded with water, which raises and lowers periodically. There are several places in this tower to visit, and each holds a different puzzle.
Statues, Switches, and Bridges
Right to the left are a few large, bombable walls as you come in to the tower. Blow them open to find a few items, and a path to enter later. From here, sail to the southeast corner of the floor. Wait for the water level to lower, and then go to the down to the door below and into the room.
Dungeon Map
Straight ahead in the next room is a Yellow ChuChu. It's electrified, so don't attempt striking it with your sword. Instead, smack it with the boomerang to discharge it and then kill it quickly. When the water raises, go to the southwest alcove to bomb it. Break the pots for some items. When the water lowers, pull the crate in the southeast corner of the gap west so it lines up with the cracked wall above. Once the water rises, bomb the wall to get some items and the Dungeon Map, which you'll need for the complex tower. After that, 4 Yellow ChuChus drop from the ceiling. If you wish, wait for the water to drain and use your boomerang to stun them and defeat all of them. If you want, you can bomb the other alcoves for more items. Go back to the first room.
Pressure Switch Door
With the Dungeon Map in hand, board the King of Red Lions again and sail to the northeast corner of the tower and hop onto the nearby ledge when the water raises level with it. There is a door here, but it's barred shut. However, a strange statue resides by the door, and an odd-looking pressure switch is nearby. Simply pick up the statue and place it on the switch to unlock the door.
A Magic Bridge
As you enter this room, a Yellow Chuchu will appear, but you can quickly kill it now that you know what to do. Below, there are several crates and a pressure switch. Drop a crate on the switch, and you'll cause a magical bridge to cross the gap above. However, it only stays activated when the crate stays on the switch, and the rising water pushes the crate off the switch. Wait for the water to rise, and then climb up the nearby ladder. Fly across the gap with the Deku Leaf, and you'll discover a statue on the altar ahead. Pick up the statue and carry it out of the room when the bridge reactivates. Doing this causes the door's symbol to glow.
More Statue Puzzles
When you return outside to the first room, don't drop down into the water. To your left is an altar just like the one in the last room where you got the statue. Plant the statue in the center of this altar, and you'll open a nearby watergate. Sail or swim through the newly-opened area until you come to a wall on the right. From here, wait for the water to raise you up to another ledge with a second barred door. This time there are two pressure switches and two statues. Place them accordingly, and move on.
Building a Crate Bridge
This room has a rather tricky puzzle to solve. In here, drop into the gap below to find several crates. Some are aligned in the middle of the gap. Push a few more in place to create a path to the platform on the other side. When the water rises, you can cross the crates to it, but there are two unlit torches you need to light. Go back to the lit torch nearby and smash the pots near it. You'll discover a few Boko Sticks. Pick up one, light it with the torch, and cross over to the unlit torches when the water rises. Lighting both torches causes a chest to appear, and you'll find a Small Key inside. Unfortunately, several Yellow Chuchus will drop into the room. Get rid of as many as you need to, and head out of the room.
Joy Pendant and the Path Ahead
Outside, you'll find the King of Red Lions awaiting you. Hop in and sail to the northwest area of the room where you blew up the walls. Let the water raise and hop over the wall. Go from here to a staircase on the right. There are a couple of Yellow Chuchus, but nothing serious. If you want a Joy Pendant, smash open the pots up ahead to find a Boko Stick. Light it and then carry it down to the torches by the locked door below before the water raises. After lighting both, you can snag a Joy Pendant from the chest that appears. Once you have the Joy Pendant, open the locked door when the water drains.
Magic Staircase
When you head into this room, several Yellow Chuchus will try to bother you. You can stun them all at once with a well-placed bomb, and then kill them all. This will cause a magic staircase to appear. Use it to climb to the altar above and grab another statue like the one you got before. Wait for the room to drain, and take it outside like the one last time. Carry it over to the altar on the right of the floor above. This statue will trigger the water fountain in the water chamber to stop flowing, revealing a secret passageway. At high tide, swim over to the passageway. You'll find it nearby from where you entered the corridor. It leads to a new room that doesn't flood.
Pressure Switch Trifecta
In here, there are now three pressure switches to activated, but only two statues. Don't even think about messing with the statue-like creature in the middle of the room. That is a Beamos, and it will try to zap you with its eye laser. Instead, take the two statues that you do have and put them on two switches. Then, get on the last switch yourself. You'll trigger several platforms to start moving, but make a Rat appear by doing so. Ride the platforms up (don't fall!), and you'll reach the main room of the temple.
The Second Floor
Upon reaching the second floor, the environment of the tower takes a drastic change. Instead of water-based puzzles, there are now more perilous puzzles to go through. The toughest of these puzzles involves the main room. Right now, only the door in the east corner of the room is open. Enter it and head forward.
=Dangerous Heights
As you head into this room, you'll encounter yet more Yellow Chuchus. Get rid of the one that blocks the narrow path ahead, and hop onto the moving platform and let it take you to the other side of the large pit.
The Command Statue
When you head into the next room, simply take the magic path over the narrow path to the other side of the room. Here is an altar with a statue on top. Next to it is a tablet that explains the statue will do as you command. Press R to call it over to you. It will lower down to you and will follow you as you move. However, you must take it across the narrow pathway below this time, and carefully, or else you'll lose the statue and have to try again. When you reach the end of the path, pick the statue up and take hop over to the door.
On the way back through the narrow pit, kill the Yellow Chuchus before carrying the statue onto the platform with you and riding it to the other side.
The Command Melody
When you enter the main room, the statue will act of its own accord and hop onto one of the four places on the large altar. When the altar raises into place, a tablet appears, and written on it is a new song. Go up onto the altar and read the tablet. You will learn the Command Melody, which allows you to control others.
As soon as you learn the Command Melody, the door opens and the statue you just placed tells you to control and bring the other statues to their altars. After speaking, the statue goes dormant and the song tablet vanishes.
It is guarded by Gohdan, a giant floating head and pair of hands.