- Chapter 1 – Temple of Fire
- Chapter 2 – Temple of Wind
- Chapter 3 – Temple of Courage
- Chapter 4 – Ghost Ship
- Chapter 9 – Wet Waters
- Chapter 10 – Having a Blast
- Chapter 11 – Chilly
- Chapter 12 – Gems
- Chapter 13 – A’mazing
- Chapter 14 – Ancient
- Chapter 15 – Times End
3.1 Optional Goodies
OPTIONAL: This entire section of this chapter is optional and it involves goodies that we can now collect with the bombs. Skip ahead to section 3.2 to continue onward with the main quest.
Return to Linebeck and set sail for Bannan Island at the northeast corner of the quadrant. Enter the cave on this island and use bombs to blow up the cracked wall. Make your way through the cave and exit on the other end.
Speak with Salvatore, the man sitting at the table in the middle of this area. He runs a cannon mini-game and charges 20 rupees to play. Salvatore explains how to play the game. Hit blue targets to get 100 points, and hit red targets repeatedly to earn 20 points per shot. There are a number of prizes you can earn depending on the scores you reach.
- Less than 1,500 Points – Green or Blue Rupee.
- 1,500 – 1,999 Points – Green, Blue, Red Rupee, or a Random Treasure.
- 2,000 – 2,499 Points – Red Rupee, Big Green Rupee, or a Random Ship Part
- 2,500 Points or More – Bomb Bag Upgrade #1. Afterward, a Big Green Rupee or Random Ship Part.
Additionally, if you beat your record, you will earn another prize. This location is a good place to earn some extra free rupees, but at the very least, keep playing until you have won the Bomb Bag upgrade. Afterward, return through the cave and head back to the boat.
Use the Cyclone Slate, or just set sail back to the southwest quadrant and head over to the Isle of Ember once again. Once you arrive, return to Astrid’s Hut and speak with her. After finding out that you have rescued another spirit, she will reward you with a 4th Wisdom Gem.
Return to Linebeck and set sail for Mercay Island. Once you arrive you can run over to the Mercay Island Shop where you’ll find that bombs are now for sale. If you haven’t already, you should go ahead and purchase the Power Gem from the store. By now you should have enough rupees to acquire it.
Make your way back to the west side of Mercay Island and speak with Oshus. Much like Astrid, he will congratulate you for getting as far as you have, rewarding you with a Power Gem. NOTE: If you don’t actually talk to Oshus at this point, he will eventually just mail the Power Gem to you in a letter.
Make your way to the north end of the island and you’ll finally be able to blow up those cracked blocks that have been blocking your way. In the area just near the entrance to the Temple of the Ocean King, there is a cracked wall that can be blown up using the bombs, so do so and then enter the cave.
There isn’t too much to do inside this cave at this point in time. You can leap across the ledges and find a treasure chest that contains another Power Gem. We will return here at a later point once we get a new item. At this point you can exit the cave and make your way back to the Temple of the Ocean King.
3.2 Temple of the Ocean King III
Your third journey through the Temple of the Ocean King will have you retrace your steps through several familiar floors. Now that you have the bombs, there are a few shortcuts to make the route a bit faster. The Temple guide below will still cover all the floors, but we’ll quickly run through some of the familiar areas, mainly pointing out the new features.
|~ Floor 1F ~|
There is nothing new on floor 1F, so run over to the staircase and head down to floor B1.
|~ Floor B1 ~|
Run over to the northeast corner of the room. Now that you have bombs you can blow up the cracked blocks to the left, allowing for quick access to much of the room. Step on the floor switch to open the door and then run over and grab the small key. Return to the locked door at the northeast corner of the room and head down the stairs.
|~ Floor B2 ~|
Wait until the Phantom is looking to the west and dash southward. There is a cracked wall to the south that you can blow up, revealing a shortcut. Do just that and the Phantoms will likely be alerted. You can run to safety at the northeast safe zone and wait for the Phantoms to retreat.
You will still need to hit the two crystal switches near the northeast part of the room. Do so and the small key will once again drop. Run over to the safe zone at the east part of the room. When the coast is clear, step on the floor switch and use the Boomerang to snag the small key.
Wait until the Phantom is heading toward the southwest corner of the room. Then quickly run southward across the lowered blocks. Hit the switch to change which blocks are lowered, and then run to the locked door to the west. Use the small key and head down to the floor below.
|~ Floor B3 ~|
Unfortunately, this floor does not have any large shortcuts, but there are a few notable changes. You will still need to collect the three Force Gems and place them in their proper slots at the top-right portion of the room. The first Force Gem can be snagged from the treasure chest at the northwest portion of the room. Once you place it in its slot, run over to the northeast corner of the room. You can use bombs to blast away the blocks and break the yellow jar for some extra time.
The second Force Gem is at the southeast corner of the room within the treasure chest. After snagging the second Force Gem, return to the southeast corner. Just to the right of the flames, there is a soft soil spot where you can dig up a geyser with your Shovel. This offers a small shortcut. Step on one of the two floor switches, causing the Phantom to fall into the abyss.
Grab the small key that is left behind and use it to unlock the door at the southwest portion of the room. Take the third Force Gem to its proper slot and then head up through the door. In the next room you can now tap on the door and Neri, the Spirit of Wisdom will open it up. Before heading down the steps, be sure to break the yellow pot on the left side of the room for some extra time. Continue down the steps to the next floor.
|~ Floor B4 ~|
On this floor you will be introduced to Phantom Eyes. If they spot you, they will slow down your movement and cause Phantoms to quickly appear. Walk down on the right side of the screen until you reach a gust jar that is blocking your way. Trace a path with your Boomerang to hit the crystal switch, causing the wind to subside. Before heading down, trace a second path with the Boomerang and hit the Phantom Eye. While it is stunned, run over and slash at it with your sword to defeat it. Be sure to also use your Boomerang to break the yellow jar at the corner of the room to acquire some extra time.
Run over to the safe zone if needed and wait for the Phantom to begin walking upwards. Follow the Phantom up and to the left, being sure not to get spotted. Once you are in the center of the room, don’t peak your head too far north, as the Phantom Eye will spot you. Instead, wait just around the corridor and toss the Boomerang at the enemy to stun it. Defeat the Phantom Eye and then run over to the northwest corner of the room. You can break the jar to create a safe zone.
Wait until the third and final Phantom Eye is moving southward and then quickly run over to the safe zone at the west end of the room. From here you can wait until the Phantom Eye comes nearby and then stun it with your Boomerang. Defeat the Phantom Eye and a large treasure chest will appear at the east end of the room. It’s a bit out of the way right now, but be sure to make note of it.
Near the southwest corner of the map, use the Shovel to dig up the soft soil spot. Ride the geyser to the higher platform and strike the crystal switch. This will cause all of the gust jars in the room to go out, making for quick navigation throughout the room. Note, while standing next to the crystal switch, if you trace a pathway northward with your Boomerang, you can hit a yellow pot for an extra 30 seconds.
Run over to the western safe zone and wait until the Phantom starts walking southward. Run to the east a bit and you’ll notice a crack in the nearby wall. Toss a bomb to blow open a hole. Be careful as the Phantom may draw near due to the noise. Run inside and strike the switch, causing the spikes on the east side of the room to drop.
Maneuver around the Phantom and run over to collect the small key. While in the area, be sure to open the large treasure chest on the right to acquire a Power Gem. With the key in hand, make your way to the locked door at the south end of the room while avoiding the Phantom. Open the door and head down to the next floor.
|~ Floor B5 ~|
Wait for the spikes to lower on the left and then run past them. There is a crystal switch at the far southwest corner of the room. Wait until the spikes lower and then smack it with your Boomerang. This will cause the spikes on the right side of the room to lower. You can run over to get 30 seconds of time, as well as replenish your health. Run back to the left and then head up, where the door will shut behind you.
Four yellow Chuchu will appear. Hit them with the Boomerang to stun them and then finish them off with some sword slashes. When all four are defeated, be sure to grab the 15 seconds of time at the west end of the room and then travel eastward.
Once again the door will shut behind you and this time you’ll be greeted by some Miniblins. Make quick due of these enemies and then collect 15 more seconds of time from the right side of the room. Run northward and use the Boomerang to hit the crystal switch to the right, causing a treasure chest to appear that contains a Red Potion. Note, if you already have two potions, this will instead have some rupees. Run over to the door and head down to the next floor.
|~ Floor B6 ~|
Once you arrive at this floor, wait until the Phantom Eye at the northeast corner comes near and smack it with the Boomerang. When the coast is clear, run over to the safe zone at the northeast corner of the room. Here you will find a massive tablet that states that it is the second tablet in the governing crest. You can make a note on your map with the number 2. NOTE: There are four tablets in this room and while you can look at all four of the tablets to figure out the puzzle, you can also just skip down in the guide to find the immediate solution, as reading the tablets is not required.
Next, if you run to the southeast corner of the room you can hit the crystal switch, lowering the nearby spikes. Read the tablet here and then mark it with a number 4 on your map. Just to the left of the statue there is a floor switch that will cause the nearby gust jar to wind down.
Just to the left of this gust jar there is a second one, but the floor switch to deactivate this gust jar is on the left. Be careful to avoid both of the Phantoms and the Phantom Eye and run along the southern end of room before then stepping on the floor switch. With the gust jar now deactivated, run to the safe zone near the large red door. From here you can target the Phantom Eye on the left with your Boomerang and then defeat it with your sword. Doing so will cause the spikes at the west end of the room to lower.
Run over to the west part of the room and break the pot to get some extra time. Step on the nearby floor switch to deactivate the gust jar found here as well, giving you quick access to the safe zone. Don’t read this tablet as it will cause two Phantom Eyes to appear in the room.
Run over to the northwest part of the room and break the red pot to create a small safe zone. Pull out your Shovel and dig up the nearby soft soil, then toss a bomb onto the newly revealed wind geyser. This will blow up the cracked blocked. Ride the geyser up and hit the crystal switch, causing the nearby spikes to lower. Read the tablet that is now accessible to find that it is both the first and last point in the sacred crest, so mark it with a 1 on your map.
The final tablet is at the southwest corner of the room and can be accessed after bombing the cracked blocks. Be careful as the bomb will alert any nearby Phantoms. This tablet is the 3rd for the crest, so be sure to mark it on your map.
Run over to the large red door in the center of the room where you will need to draw the crest. The pattern matches the order that the tablets in the room gave. In one stroke, place your stylus at the top-left, move it to the top-right, then to the bottom-left, then to the bottom-right, and finish off back at the starting point at the top left. The shape is that of an hourglass and correctly drawing it will cause the door to open, so head on through.
Climb the steps and walk up to the sun symbol. You have to press the crest up to your map. If you look closely, the image is actually an upside image of the southwestern quadrant. Pull up your Sea Chart and select the southwestern quadrant. At this point you need to close your Nintendo DS/3DS. Yes, actually close the clam-shell. Note: If you are on the Nintendo 2DS you will need to just put your system into sleep mode. Doing so will cause the symbol to appear on your map in the middle of the sea. Step into the blue warp portal to return to the temple entrance.
Back outside, run on over to Linebeck and along the way, you’ll notice the Mailbox is shaking. There is a letter from Eddo at Cannon Island. He mentions that he has been working on a Salvage Arm and it is now ready. Walk towards Linebeck and one of the villagers will call you over, also letting you know of the Salvage Arm. Finally speak with Linebeck and set sail.
3.3 Salvage Arm
Set sail for Cannon Island and then enter the building to speak with Eddo. He wants you to shout about how much you want the Salvage Arm. This involves you yelling or just blowing into the Nintendo DS microphone. Depending on how loud you yell, Eddo will sell you the Salvage Arm for a cheaper price. The cheapest you can get the item for is 200 rupees, but you could pay up to 1,000 rupees if you don’t yell loud enough at all. After acquiring the Salvage Arm, return to the ship and set sail.
Now that you have the Salvage Arm, set sail for the green crest that is in the middle of the quadrant. Once you arrive, tap the Menu button and select the Salvage icon. This will release the Salvage Arm down to the depths of the sea. Unlike in The Wind Waker where Link would just pull up the treasure automatically, this time you’ll have to do some work.
Drag the bar to the left or right to move the arm side to side. Tap the red scroll upward to slow down the rate at which the arm is dropping or tap the red scroll downward to speed things up. Your Salvage Arm has its own health bar, indicated by the yellow diamonds at the top-left of the screen.
As you lower the Salvage Arm, you’ll run into a number of obstacles. Underwater you will find stationary Octomines that will explode if you hit them with your Salvage Arm. Additionally, you’ll find some Octomines that move left and right, sending a gust of water towards your arm, which will cause it to sway, potentially hitting another mine or wall.
While salvaging for treasure, there are a number of rupees that can be collected, however, they are often found in dangerous areas between Octomines. Once you reach the bottom of the sea floor, position your salvage arm above the treasure chest to grab it. Now carefully pull it back up, avoiding the Octomines. Successfully doing so will earn you the Sun Key!
Now that you have the Salvage Arm, an event has been triggered back at Mercay Island, so sail on over. Speak with the man who is standing right next to the dock. After telling him that you have the Salvage Arm he will offer to sell you a Treasure Map for 50 rupees, so go ahead and snag it. This now marks the 9th Treasure Map that you have collected up until this point. It’s now time to get the Sunken Treasure.
Of the 9 Treasure Maps, only 8 of them are accessible at this point. The 4th Treasure Map is marked by an X that is southeast of Bannan Island. You won’t be able to access this treasure until you can first reach the Northeast Quadrant. The locations and goodies of the 8 Sunken Treasures are listed below. NOTE: If you bang up your Salvage Arm, you can get it repaired at the Shipyard on Mercay Island.
Your rewards include 5 ship parts, a treasure, and 2 additional minutes of sand for your hourglass. There are a ton of rupees to collect as well. For the most part, you should avoid any hard-to-reach rupees, with the exception of the big green rupees as those are worth getting.
3.4 Molida Island
It’s now time to return to Molida Island, so sail on over. As you draw near you’ll be confronted by a Giant Eye Plant which is blocking the entrance to the island. The weakness of this giant enemy is its eye and you’ll need to hit it with a number of cannon shots. Your best bet is to draw a half-circle, going back and forth around the Eye Plant. Draw it so that the pathway overlaps itself over and over so that you don’t have to worry about sailing and instead can just battle the enemy.
The eye plant will launch green spiky balls out towards your ship. These can be defeated with a single cannonball shot, so be sure to hit them quickly as they will otherwise harm your ship. Wait until the eye of the enemy is open and then launch an attack to hit it. After a number of hits, the enemy will be defeated and Link will pull up to Molida Island.
Once you arrive at Molida Island, once again dig up the hole that you dug up during your first visit to the island. It located just south of the palm tree between the 2nd and 3rd huts on the island. Run northward and tap on the door to use the Sun Key. Continue northward and exit the cave to find yourself at the north end of the island.
Once you are outside, use the shovel to dig up the mark in the grass just to the left. This creates a secret hole so go ahead and drop down. Open the treasure chest you find here to collect a Wisdom Gem. Leap off the ledge and once again exit the cave.
Defeat the Miniblins and yellow ChuChu on your way to the north end of the island. You will arrive at the Temple of Courage but the door is locked. The nearby tablet tells you that the statues must focus their light gaze on the door. Continue to the right and you’ll find a statue. Strike it with your sword to activate it, and then tap on it to turn it. Rotate it so that it is facing northwest, causing the beam of light to shine on the locked door.
Run to the south and west and you’ll bump into a pair of Zora Warriors. Stun them by hitting their backs with a Boomerang and then finish them off with a number of sword slashes. Once they are defeated, another statue will appear. Activate it and then turn it so that it is facing northward, shining the light onto the door.
Leap off the ledge to the left and then climb the small steps nearby. While on the higher platform, if you glance to the southwest, you will find the third and final statue. This one is already facing in the proper direction and you just need to activate it. Use your Boomerang to hit the statue, causing it to shine its light onto the locked door.
With all three lights now shining, the door will open up. Run on over and head inside to take on the next dungeon, the Temple of Courage.
3.5 Temple of Courage
|~ Floor 1F ~|
Maneuver around the rolling spikes to reach the north end of the room. You’ll find a suspicious looking wall to the north which will explode if you throw a bomb at it. Run over to the treasure chest and open it up to get a random treasure.
Follow the pathway southward and you’ll run into a blade trap. Move towards it to trigger its motion, then quickly run southward. Step on the floor switch here to open up the nearby door, creating a shortcut. Climb the steps to the north and open the treasure chest to get a small key. Leap off the ledge to the right and make your way over to the locked door at the north end of the room.
Run southward and the door will close behind you. A pair of Moldorms will appear, whose weak spot is the large red portion at the back of their body. Deliver sword slashes when you can, but then move away when the enemy charges at you. Defeat both enemies and then head down the steps.
|~ Floor B1 ~|
Wait until the moving platform has come nearby and then walk onto it, riding it westward. Hit the Shell Beast on the platform so that you knock it off the ledge and then step onto the next platform. While riding the platform, use the Boomerang to hit the nearby crystal switch, changing it to red. Then step onto the next moving platform and ride it westward. Climb up the steps here to get back to the first floor.
|~ Floor 1F ~|
This room is filled with Slime enemies as well as a new enemy Winder. These electric enemies cannot be defeated and should just be avoided. Run to the north end of the room and you’ll find a pair of tablets. One will give you advice on how to beat an upcoming enemy, while the other one states that “Up, Down, Right, then Left” is the order for the whole temple. Be sure to take note of it.
Next to the tablet on the left there is a suspicious wall. Toss a bomb to blow it up and then open the treasure chests on the other side to get a Ship Part and a Power Gem. Glance at the wall and you will see a picture of a map with a route on it. Pull out your map and switch over to floor B1. Trace the path of the red line onto your map for future reference.
Bomb the cracked blocks to the ride and continue to the next part of the room. Here you will find a green chuchu. This variant of the enemy will shrink into a tiny puddle when you try to attack it with a sword. Instead, stun it with a boomerang and then defeat the enemy.
South to the southern platform and a giant Pols Voice will appear. These enemies are invulnerable to Link’s sword at the present moment. You will need to blow into the microphone, causing them to shrink into a tiny ball, making them vulnerable to attack. After defeating the enemy, grab the small key it leaves behind. Be sure to step on the nearby switch, causing the door to open and creating a shortcut to the dungeon entrance. Use the small key on the locked door above and climb the steps to get up to the second floor.
|~ Floor 2F ~|
In this room there are four pullable levers and this is where the hint about the order of the dungeon comes into play. Be careful as the room is filled with winders and beamos statues, neither of which can be defeated. You have to pull the levers in the proper order. First pull the one at top, then the one at the bottom, followed by the one to the right, and finally the one to the left.
When all four levers have been pulled a treasure chest will appear in the center of the room. Open it to get the square crystal. Much like when holding the Big Key, you won’t be able to move as quickly while carrying this item. Carry it back to the staircase and head down to the first floor.
|~ Floor 1F ~|
Back on first floor, climb up the nearby steps and place the crystal onto the square pedestal. This will cause one
of the nearby doors to open up so run on over and head down back to floor B1.
|~ Floor B1 ~|
There are invisible floors that exist in this area that you can walk on. This is the floor that corresponds to that map we saw earlier. For reference, you can see the path traced on the map below. Carefully make your way through the area, disposing of the enemies along the way. Be careful as the shell beasts will try to bump you right off the platform.
NOTE: in the center of the large map, there is a small platform with a treasure chest. There is an invisible pathway that leads to this treasure chest, so be sure to make note of it. Open the treasure chest to get a big green rupee.
At the end of the pathway open the large treasure chest to get the dungeon item, the Bow and Arrow. Equip the arrow and shoot the eye target that is along the northern wall, causing a bridge to extend to the south.
Cross the bridge and you’ll encounter a Moldorm. Now you can defeat this enemy with a single arrow shoot to its red weak point. Just to the right you will see an object known as an arrow orb. Slash at it with your sword until it facing eastward. Now pull out your Bow and shoot the arrow orb which will cause an arrow to be launched to the right, and then down, hitting the crystal switch and turning it red. With the switch now read, climb the steps to get back to floor 1F.
|~ Floor 1F ~|
With the blue blocks lowered, run southward and defeat the two moldorms. Walk to the far right and use the bow and arrow to shoot the eye statue, causing one of the nearby doors to open up.
Run back to where you placed the square crystal and pick it up off its pedestal. Carry the square back to the southwest corner of the room and place in the other pedestal that is found here. This will cause one of the nearby doors to open. Climb the steps to get back up to floor 2F.
|~ Floor 2F ~|
In this room there are a number of octoroks, some of which are across the gap to the south. Defeat the nearby ones with your sword and then use your bow to shoot at the other octoroks. With all of them defeated, a bridge will appear, extending across the gap.
Cross the bridge and step onto the moving platform. Ride it to the southwest corner of the area and then make your way over to the next moving platform. From here aim with the bow northward and hit the eye switch.
Step onto the moving platform that is going and up and down, and then onto the next platform moving left and right. From here you can hit a second eye switch to the north, causing a treasure chest to appear. Ride over to the treasure chest and open it up to get a Power Gem.
Follow the moving platforms to the right side of the room and then run by the first two blade traps to find a beamos statue. Take the pathway to the left of the beamos statue and then use a bomb to blowup the cracked block.
Now take the pathway on the right side of the beamos and grab onto the movable block. Wait until the blade trap is on the right side and then push the block downward. Backtrack around and then push the moveable block all the way to the right. Open the nearby treasure chest and then head back down the steps.
|~ Floor 1F ~|
Back on the first floor, simply walk to the west, avoiding the two winders in the room. Step on the floor switch, creating quick access to the entrance of the dungeon. Then head down the steps to get down to floor B1.
|~ Floor B1 ~|
Ride the moving platform to the right and then step onto the stationary platform. Use the boomerang to target the lit torch and then target the unlit torches to light them up. There are six torches in total and the bottom four can all be lit from the stationary platform at the bottom-right portion of the screen. Ride northward on the moveable platform and light the final torches, causing the nearby spikes to lower, giving you access to the next platform.
Hit the shell beasts so that they fall off the platform and then turn to the left to find an arrow orb. Hit the orb with the boomerang twice, causing it to face to the west. Shoot an arrow at the orb and it will then hit a couple of arrow orbs before then hitting a crystal switch, causing the red blocks to be lowered.
Before heading up, once again toss the boomerang at the arrow orb, causing it to face northward. Once again shoot it with an arrow, and this time it will hit a number of orbs and then an eye switch. This will cause a nearby treasure chest to appear containing a wisdom gem. Grab it and then head up the stairs back to the first floor.
|~ Floor 1F ~|
In this narrow corridor a pols voice will drop down from the ceiling. Blow into the microphone to defeat the enemy and it will drop a small key. Use the small key on the locked door and then head up to the second floor.
|~ Floor 2F ~|
Step onto the blue block and then take a glance at your map. There are four pillars in this area and each of them has an eye target on it. You’ll have to hit the targets in the proper order. This room follows the order of the dungeon, which was also used to solve a puzzle at the northwest part of the floor earlier on. Remember, the order is Up, Down, Right, and then Left.
To move along on the blue platform, pull up the map and trace a pathway, which will cause the block to move. Be careful not to cause too many intersections as it will confuse the direct that you need to go. Additionally, you are standing a large block, so don’t draw your lines right into the pillars. At anytime you can pull up your map and erase the lines that you have drawn. Then you can redraw lines to move wherever you need to go.
Once all four eyes have been hit, a treasure chest will appear at the top-right portion of the room. Make your way on over and open the treasure chest to get the big key. Step back onto the platform and ride it to the southwest portion of the room. Use the key on the locked door and head up to the third floor.
|~ Floor 3F ~|
Read the tablet to create a blue warp portal that will take you back to the entrance of the dungeon. Slash all the nearby pots to collect some extra arrows and hearts. Before walking up the staircase, walk to the north end of the room where you will see a cracked wall and a treasure chest on the other side. Blast open the wall with a bomb and then open the treasure chest to get a courage gem. Once you are ready, climb the steps to take on the dungeon boss.
During the first phase of the battle there are smaller Crayklings scattered around the ground floor. These small creates can be defeated with two sword slashes and will leave behind arrows and recovery hearts as a reward. Try to keep your distance from Crayk, but he if he comes into contact with you, he will deal damage. Crayk will also grab Link and shake him, causing there to be continuous damage each second. Rub the stylus on the bottom screen quickly to break free.
During this initial phase, Link will need to hit Crayk with an arrow. When you see Crayk looking directly at Link in the top screen, turn around until Link is directly facing the camera and then shoot an arrow in that direction. It can be a bit difficult at first and shooting a number of arrows repeatedly in the general direction should help you hit Crayk.
After Crayk has been hit, he will begin to spin around and becomes vulnerable to attacks. You’ll notice the small purple spheres sticking out from parts of its body. These are its weak points and you can either hit them with your sword, or aim your bow towards them. He moves pretty rapidly, so it is a bit difficult to be precise and sometimes just spanning sword attacks is your best bet. After hitting all the purple spheres, the first phase will be complete.
Crayk has now lost his invisibility and the large blue tail is his new vulnerability. He turns fairly rapidly so it at first appears hard to reach his backside. Slash at his head and he will cover up his face in defense. This will give you time to quickly run around back and slash at the blue spot. Repeat this process until Crayk has been defeated.
After defeating Crayk, Link will collect two more minutes of sand into his hourglass. Link will also meet with the Spirit of Courage. After an awkward talk, be sure to open the treasure chest to get a Heart Container. Step into the blue warp portal to get back outside of the dungeon.