After getting the Regal Necklace from the Isle of the Dead, you will be able to reach the Isle of Ruins.
Reach the Isle of Ruins
Go north from the ship and enter the cave. As you go through the cave, the door will close behind you and you have to defeat a Zora Warrior. Try using the boomerang to stun it before you attack. After it is gone, a bridge extends to the north. Cross the bridge and read the sign. Then follow the path out of the cave.
Go south from the cave exit, then go west across the bridge. Jump west across the short gap, then go north along this strip of land. When you can't go farther north, jump west across the short gap.
From there, go south until you can't go any farther south, then jump west across the gap. Go south, then west, then north, and jump over the gap to the west. Go north, then when you can't go any farther north, jump east over the gap. From there, go north and cross the bridge to reach another area of the island.
Jump down from the east side of the ledge, and kill the Stalfos that jump out. You can go west and north, and kill the Rupee Like, then dig the brown spot on the ground to get a giant green rupee.
Then go south and east to where you fought the Stalfos earlier. Go east and up the stairs, then west, and you will enter a path with rolling boulders. Avoid them as you go north. At the end, go up the stairs. The path will lead you to the pyramid in the northwest corner. Go inside.
Go north and approach the sarcophagus, then tap Bremeur to talk to him. Say yes when he asks if you need something from where King Mutoh sleeps. Say yes when he asks if you can calm Mutoh's rage.
Go outside and a new bridge will appear. Go cross that bridge. Go east from the bridge and do a roll attack into the tree to get a big red rupee. Then go down and kill the miniblins, then go east, killing more miniblins on the way.
In the next part of the island, go east, avoiding the Stalfos bones, then go north to the northeastern pyramid.
The west side of the pyramid has rolling boulders. Then the path down the middle has arrows that shoot from the walls. When you go northeast to the eastern corner of the pyramid, stay close to the wall to avoid the trap door in the floor. Go up the stairs and cross the bridge, then go south and go up the stairs.
Tap the door to open it, then go north to the sarcophagus and tap the ghost to talk to Doylan. He will give you the King's Key.
Go south to the first floor, then go south and fall off of the ledge to reach the exit.
Outside, go west, then north across the bridge, killing the Stalfos that blocks the way. Go west from there to return to Bremeur's Temple. Inside, tap the golden obelisk to use the King's Key in it. After the cut scene, go outside.
Go east off of the ledge and make your way east along the new path. Go as far east as possible to find a treasure chest that contains a big green rupee. After that, go west, then south. Go east from there. You will find a boulder on the left that you can't push, and a boulder on the right. Push the boulder on the right until you can go past. Then go up the stairs and push the boulder to get rid of the boulder on the left. Go down there and go past where the boulder was. Go south from there.
Kill the two Stalfos, then go east. Push the boulder up once, then push it to the right until it rolls down the stairs. Go east across the bridge, throw the small boulder, then go north to find a chest that contains a Wisdom Gem.
Go back to where you rolled the boulder. This time, push the boulder to the right, then push it down until it destroys the boulder to the south. Throw the small boulder and go south. There is a switch on a ledge nearby. Step on it to create a shortcut back to the dock.
Then go clockwise around the pyramid, and go inside. Go north to the sarcophagus and tap the ghost to talk to Max. Say yes when he asks if you will undergo his trial. He says that he will open the door where you can learn the secret crest to draw in Mutoh's temple.
Go outside and go through the door that opens. Read the sign inside. It mentions the surface maze. This is referring to the maze in the southwest part of the island. Go west of Max's pyramid and cross the bridge that leads to the dock (step on the switch if the bridge is not there). From there, go west to the maze.
Now that the water has lowered, you can reach the stone tablets in the maze area. Be careful to avoid Rupee Likes as you go through the maze. The first stone tablet is in the northwest corner of the maze area. Go east from there to find the second tablet. Go south from there to find the third. Go northwest from there to find the fourth. Go southwest from there to find the fifth. Go north from there to return to the last tablet. That is the pattern that you have to draw on the red door in the southeast part of the island.
Go to the northwest stone tablet and go north, then east, and go back to the red door and draw the crest as described.
1---------2 6 | | | | 4 | | / \ | | / \ | 5 / \ 3
After the door opens, go north, kill the two Stalfos, then go north and tap the door to open it, then go north and kill the two Zora Warriors. The door to the pyramid will open. Go in.