After completing the Goddess's Silent Realm, you receive the Stone of Trials, which gives you access to Sky Keep.
Open the blue chest straight ahead to get the dungeon map. The bars nearby will go down, and Fi will mark the triforce parts on the map. Go through into the area that the bars were blocking.
Examine the tablet near the door. In this sliding tile puzzle, you can slide the tiles to rearrange the layout of the dungeon. However, you can't reposition the room that you are in, so for that reason, you can only slide the right tile down and the middle tile to the right. You can also move the green Triforce's room to the top-right corner, but you won't be able to do anything in there, so don't bother.
Note: The rooms in Sky Keep represent the dungeons from earlier in the game. You can tell which dungeon each room represents by listening to the music. The rooms in the diagrams on this page are named based on the music that plays in each room.
After rearranging the tiles in the puzzle tablet, you can go through the door next to the sliding tile control panel to reach the Skyview Temple Room.
Go to the right, kill the babas, then use the beetle on the rope across the gap. Use the whip on the whip pole, then swing onto the rope that you just cut down, and swing to the other side of the gap.
Do a side slash to make the skulltula spin, then hit its purple belly with a thrust to kill it.
Use the clawshot on the rotating vines, then use it again on the other set of rotating vines while avoiding the furnix. Use the clawshot on the target on the wall. Then use the beetle to catch a bomb from the rotating vines and make it explode on the middle of the fire-breathing monsters to kill all three.
Run and jump onto the swinging rope to reach the wooden platform. Use the gust bellows to make the platform swing so you can run onto the other wooden platform. From there, use the gust bellows to swing the platform so you can jump to the ledge.
Pull down the red bar to give yourself a shortcut. Strum near the butterflies to reveal a goddess wall. Finally, go through the door near the bird statue.
Take the timeshift orb, killing the Technoblins that appear. Carry the orb through the barrier. Kill the Sentrobe, then climb the ladder and pull down the red bar up above. Go down and step on the switch. Throw the orb onto the conveyor belt, then go up and step on the switch to retrieve it.
Stand on the moving platform and put the timeshift orb onto it. Use the gust bellows to move the platform until it stops at the bars. Jump off and walk over to the red button. Step on it, then use the gust bellows to move the platform past where the bars were. Go to the left and keep moving the platform until the barrier on the wall disappears and you can shoot the target.
Go through the bars, then pull down the red bar and get the orb. Continue to the next area.
Put the orb onto the conveyor belt and kill the beamos. Hit the five wall targets with the bow. This gives you access to another sliding tile puzzle tablet. Get the orb, then rearrange the rooms with the control panel.
After rearranging the tiles as shown above, go south to the Skyview Temple room, then go west to the Earth Temple room.
Go under the red arch and kill the red chuchus that appear, then crawl into the small gap in the left wall. Go to the left to a room that contains bombs. From this room, roll a bomb into the passage. After bombing the rocks, crawl through the passage.
Kill the large red chuchu, then burrow into the hole in this room. Hit the red switch to move the gate out of the way. Go back to the spot of light that you started at and climb back out. Crawl into the hole in the wall, then turn left and go out.
Turn left and run forward. Kill the lizalfos, then throw a bomb into the statue's basket to knock it down. Then stand on the round platform and roll a bomb down the ramp to knock down another statue.
Slide down the ramp to go into the area that the statue was blocking. Hit this switch. Climb up the vines in here, then shoot an arrow at the bomb inside of the circle of trees. After a new bomb grows there, use the beetle to grab it and drop it into the statue blocked by trees on the far ledge.
Now you have to activate the three switches in order from lowest to highest. To save arrows, use the beetle to hit the switches. The correct order to hit the switches is: the one at the bottom of the ramp, then the one that was near the lizalfos, then the one that was behind the trees.
After doing it correctly, go down the ledges to the right and jump across to the area where you fought the lizalfos. Go past where the bars were and dig into the burrowing hole. Hit the bomb twice to break the rocks on the right, then when a new bomb grows, hit it to the left, then hold the A button to run below it and hit it up to the rock above. Switch the gate, then go back to the same burrowing hole that you came in through.
Go back out of this area and turn right, going under the red arch. Go through the door to the left of the gate. Dig into the burrowing hole here. Kill the two moldorms, then crawl out at the upper-right corner. Pull down the red bar to give yourself a shortcut, then exit through the north door.
In the next room, you will fight a mini-boss, Dreadfuse. He is similar to Scervo.
At the start of the battle, hold A to run toward him, then hit him as soon as you get close. If he blocks your attack, do a backflip to get out of the way of his counterattacks. Sometimes he attacks multiple times during a counterattack. After he's done attacking, run in and hit him. If he electrifies his sword, be sure to swing the sword in the proper direction to avoid hitting his sword. Don't be hasty. If he gets too far away from you, hold A to run toward him. Once you hit him to the edge, he will lose one of his swords, but he'll pull out a second one.
Run toward him again at the start of the second phase. His counterattacks are worse after he starts using the second sword. Otherwise, just keep pushing him back until he reaches the edge. His arm will explode, leaving him with only the hook.
He can electrify the hook, so be sure not to hit it with your sword. Just keep hitting him back and do backflips to stay out of the way of his counterattacks. After you knock him to the edge the third time, he will fall and die.
Use the clawshot on the target on the far wall, then open the chest to the right to receive the key.
Now turn around and go through the door to find a sliding tile puzzle control panel. Rearrange the rooms as shown below.
Now go through the west exit, then the south exit to get to the Earth Temple room.
From the Earth Temple room, rearrange the rooms as shown below.
Go through the north exit to reach the Ancient Cistern Underground Basement room.
After defeating Dreadfuse and getting the key, you can unlock the door in the Ancient Cistern Basement area. Up ahead, there are iron shield moblins. You have to kill them to get to the next part, so run up their shields to get behind them, then hit them repeatedly until they die. You might be able to make them fall off by hanging off of the side of the narrow walkway, but it is risky and might not work.
After you kill the iron shield moblins, the door to the next area will open. Go through. Kill the bokoblins and stalfos in this area. Try using your bow to kill the bokoblins before you deal with the stalfos.
After that, the next door will open. Kill the cursed bokoblins first. Remember that they won't die unless you hit them with a fatal blow. Then kill the four-armed stalfos warrior.
In the next room, stand on the mark on the floor and press A. Then follow the on screen instructions to reach a special room where you will find the Triforce of Courage.
Back in the Ancient Cistern room, pull down the red bar to create a shortcut. Then go through the eastern exit.
Go to the left and knock down the water fruit with the beetle. Hop onto the floating platform. Kill the fire keese, then use an arrow to activate the pink switch up above.
As you get close to the short bars on the right, shoot down the water fruit. Wait until you're close enough, then hold A to run and jump onto the second floating platform.
Turn to look down the passageway and you will see a second lava flow with a pink switch on the top. Turn off that lava by shooting the pink switch. Jump off at the end and pull down the red bar to give yourself a shortcut to the entrance and bird statue.
Shoot down the water fruit and hop on. Kill the dark keese, then shoot the pink switch to the right and shoot down another water fruit. Jump onto the platform that appears. Jump onto the rising platform at the end. Use the beetle to hit the pink switch again. This makes the lava flow switch to the other side. Knock down the water fruit up ahead and jump onto the platform that appears.
Jump onto the grating to avoid getting pushed off of the platform. Use a bomb to kill the cursed spumes in the way. Use the clawshot at the end to reach a ledge. Stand on the mark on the floor and press A, then follow the on screen instructions to reach the area where you receive the Triforce of Power.
Back in the Fire Sanctuary room, pull down the red bar, then climb up the vines and pull down this second red bar to give yourself a shortcut.
Go through the east exit of this area.
The final room of this dungeon represents the Sandship. Use a bomb to kill the electro spume, then go up the ramp and get the timeshift orb. Take it to the middle of the room and set it down, killing the Sentrobe that appears.
Next, take the timeshift orb close to the barrier on the upper wall, then go back to the ramp where you got the orb and shoot the target that you revealed on the wall.
Go back and get the orb and go through the bars that were lowered. Kill the babas along the path, then leave the orb behind and step on the red switch to open the path to the target, then shoot it through the inactive fan. If the fan is on or a barrier is in the way, you have to move the timeshift orb farther back down the hallway.
After shooting the second wall target, take the orb and put it down on the ground under the cage with the nayru symbol on the floor. Put the orb down such that the barrier to the left of the clawshot target disappears, and a platform also rises that you can jump onto to reach the clawshot target. After you have put the orb in a good spot, run up the ramp, jump onto the platform, then use the clawshot to reach the cage. Step on the mark on the floor and press A, then follow the on-screen instructions to reach the area that contains the Triforce of Wisdom.
After obtaining the third piece of the Triforce, a long cut scene will take place. You won't be able to save or return Skyloft for a while, so be sure to prepare yourself. Then go through the Gate of Time to return to the past.