The Southwestern Sea
Before you can enter Molida Island, though, you are attacked by a Giant Eye Plant. Stay moving while fighting it. I advise drawing a route that goes back and forth around the plant multiple times. While you're moving, the Eye Plant will shoot three spiked balls at you - shoot these out of the air. Shoot at its vulnerable eye when it opens. It should go down after 5 hits to the eye. Dock at Molida Island.
Molida Island
Hopefully you still have the lines drawn on your map revealing where the second hideaway is. Dig at the base of that tree and jump into the hole. Head north to the sun-emblazoned door. Tap it to open it. Head all the way north to the stairs. Dig the cracked patch of earth to your left and jump down the hole. Open the chest for a Wisdom Gem, jump off the left to the right, and go back up the stairs. Follow the path, killing Miniblins and yellow ChuChus along the way. Head up the stairs, watching out for the Takkuri bird in the tree. Go north across the bridge. The tablet says that "only statues can urge the temple door open, so focus their light gaze on it!" Run to the right and around the bend, watching out for Takkuris. Hit the statue you come across to activate its laser. Tap it again and turn it so its laser beam (visible on the map) hits the temple. Continue along the path and defeat the two River Zoras that appear. Remember, use the boomerang to stun them. Once they die, a statue emerges from the ground. Hit it and turn it so its laser points to the temple. Jump off the ledge to the left, go up the stairs, and go to the northwestern edge of the platform. Hit the statue to the southwest with the boomerang. The temple door should open, so make your way to the temple.
Temple of Courage
Floor 1
Go north to the intersection blocked by doors. Don't rush north just yet, as there is a spiked roller traveling the north path. Wait for it to go north past the alcove, then hide in it until the roller passes by again. Then do the same for the next roller, ending up in the safe area between two rollers. Two tiles over, you will notice a passageway dead-ending at a discolored tile in the wall. Throw a bomb at this piece of the wall. When it's safe, run up the passage to score a piece of treasure from the chest. Wait for the roller to pass to the left, then run to the right and south. Stop by the two blocks. Walk straight south of the gap next to the blocks and note the blade trap. These blade traps will shoot straight towards you if you stand in any cardinal direction of them (that is, north, west, east, or south of them). Staying close to the blocks to the north, run quickly to the left to trigger the trap and get out of the way. Run quickly past the gap it leaves in the blocks before it resets. Hit the floor switch to the left and go up the stairs. Cross the bridge to the north and get the key from the chest. Jump off the bridge's right side and, while avoiding the blade trap and the roller, make your way to the locked door to the north and open it. Go south to a room where you have to fight this temple's miniboss, two Moldorms. Hit their pink tail ends with your sword until the Moldorms die. Go down the stairs.
Floor B1
When the platform arrives at the ledge you're on, hop on and ride it to the next platform. Here you meet the Hardhat beetle. You can't kill it with your sword, so you have to smack it off the ledge with your sword. Ride the platform to your left. Hit the switch with your boomerang as you cross. You'll have to switch platforms midway. Go back up the stairs.
Floor 1
Kill or avoid the gels while avoiding the electric Winder enemy. The Winders are indestructible, so just leave them alone. Go north past the blocks. The two tablets tell you that "Big monsters with big ears are hugely vulnerable to loud sounds..." and "Up, down, right, then left. It's not only the order for the switches nearby. It's the very order of the whole temple, so take note of it..." Do so. Bomb the discolored tile between the two tombstones to access a room with two chests containing a ship part and a Power Gem. The map on the wall shows a path for a section of floor B1. Draw this on your map, it will be useful later. Go back into the previous room and bomb the rocks to the right. Go right to find a Green ChuChu. The green ones have an annoying tendency to melt into an un-hittable puddle, so stun them from a distance with the boomerang first. Run all the way south, noting the square gem pedestal on the platform you pass to the right. Run right and hit the floor switch. Run up the stairs and a huge Pols Voice drops down from the ceiling. Remember what the tablet said about monsters with big ears? Scream/blow into the microphone to stun the monster. Kill it with your sword and grab the key it drops. Go all the way back north and open the locked door. Go up the stairs.
Floor 2
This maze contains several Winders and Beamos statues. Beamos statues will shoot a laser at you if they see you with their eye. You can disable them for a short time with a bomb. Now, keep in mind what the tablet said about up, down, right, then left. There are four switches here, and that's the order you need to pull them in. A chest will materialize with the square crystal. Take it down the stairs.
Floor 1
Throw the square crystal into the square pedestal. Go down the stairs that are revealed.
Floor B1
I hope you drew that path from the wall onto your map, because you're going to have to follow it. Follow the invisible path, knocking off the Hardhat beetles along the way. Open the chest to get the bow and arrow. Tap the screen while the bow's equipped to shoot arrows. Keep the stylus held down to look around the surrounding area. If you're using the trigger to access the bow and arrow, you can release the trigger after you're done looking around to put it away without shooting an arrow. Shoot the eye next to the chest and go south on the bridge. Kill the Moldorm and hit the crystal thing until it points right. Shoot an arrow into it. These crystals will redirect an arrow shot into them to the direction that they're facing. Watch the arrow fly into the switch and go upstairs.
Floor 1
Go south and kill two Moldorms and a green ChuChu. Go all the way east to the gap. Shoot the eye with an arrow. Run up to where the square crystal is. Grab it and head back to where the Moldorms were. Place the square crystal on the pedestal and go through the stairs that are revealed.
Floor 2
Now would be a good time to use the bow and arrow to clear out some of the enemies, as there are a lot of Octoroks spitting rocks everywhere. Once all the Octoroks are dead, a bridge extends. Cross it. Hop on the platform and ride it south. Transfer across to the next platform. There's an eye way to the north you can hit while crossing - use your bow and arrow's aiming ability to see it. Cross over the the easternmost platform and hit another eye way to the north, making a chest appear. Watch out for the Keese. Cross back to the middle platform and ride it to the chest, which contains a Power Gem. Ride the platforms over to the easternmost platform. Get off and carefully walk past the blade traps. Hop south across the gap and bomb the block. Retreat into the corridor to avoid the blade trap. When the blade trap moves away from you, run quickly to the passageway going north. Open the chest for treasure and go down the stairs.
Floor 1
Avoid the Winders, making your way left. Hop across the gap, hit the switch, and go down the stairs.
Floor B1
Ride the platform to the east. When you get on the platform going north, equip your boomerang and try to light all of the torches in one go. I made a zigzag pattern hitting them in this order:
65 34 21
This retracts spikes to the north, allowing you to get off. Knock off the two Hardhat beetles, then use the boomerang to hit the crystal until it points left. Shoot an arrow into it. Hit it with the boomerang until it points up and shoot another arrow into it. Grab the Wisdom Gem from the chest that appears and run up to the stairs in the north.
Floor 1
Another Pols Voice appears. Again, scream/blow into the microphone and kill it. Grab the key and unlock the door. Go up the stairs.
Floor 2
The gossip stone tells you that the platform is controlled by a path you draw on your map. So bust out the map and draw a path. Now, each pillar on the map has an eye on its south side. And remember that up down right left is the order of the whole temple. Thus, your path should pass to the south of the north, south, east, and west pillars in order. It should then end back where you started. Hit each eye with an arrow as you pass by. Once the eyes are hit in the correct order, a chest spawns with the Boss Key. Now draw a new path heading straight to the southwest platform. Get on the platform with the Boss Key and ride. Open the boss door with the key and go up the stairs.
Floor 3
Break the pots for arrows and health. Go behind the stairs and bomb the cracked wall. Go through the hole and open the chest for a Courage Gem. Go up the stairs to face the boss.
Boss Fight: Crayk, Bane of Courage
This battle starts off with Crayk turning invisible. However, the top screen becomes what Crayk sees. It's best to lightly move around rather than go move crazy. Since the top screen shows what Crayk sees, when Crayk sees Link, he'll charge toward Link which will be done after a blow of the wind. Prepare the bow and then circle around Link with the stylus until you see Link on the top screen directly pointing at it; that is when you let go to hit Crayk.
Crayk will retreat into his shell and start spinning slowly if you hit him. Hit the six purple spheres on his shell to break the shell. While fending off the smaller crabs that attack, shoot arrows at Crayk's face. This will cause him to hold still and guard, so use this time to circle around him and attack his tail. Rinse and repeat for the victory.
The Aftermath
Crayk will dissolve into some Sand of Hours. Grab the heart container that appears after the oddly lethargic Fairy of Courage joins you and step into the portal.
Molida Island
Return to Linebeck's ship. On the way, you may notice a change in Romanos' hut. He's decided to follow his father's footsteps and become a wayfarer, but he needs to raise money, so he's running the shooting range, by far the hardest minigame in the game. He will also have sent a letter with a ship part, so stop by the mailbox on the way to Linebeck. Also, now that you have the bow and arrow, you can buy a quiver upgrade from any village shop for 1000 rupees. You must have bought the Power Gem first. Oshus is waiting at the dock, who reveals that Ciela is the Spirit of Courage. The lethargic fairy you found in the temple was half of Ciela that contained her powers. Using his magic, Oshus fuses both fairies together, turning Ciela into her true yellow color. Ciela senses Tetra calling out to Link, and the boat sets sail.