The Legend of Zelda: Phantom Hourglass/Discovering the Southeast Sea

Mercay Island
You'll receive a letter from Linebeck with a random ship part. Head to the Temple of the Ocean King and head to floor B3 via the same path as before. Many of the Phantoms have now been replaced with Swift Phantoms. These red behemoths move much faster than regular Phantoms, so be aware. Also, Phantoms share the Reapling's weakness to being shot in the back with an arrow.

Floor B3
Clear B3 as before. Instead of going through the door, however, go back to the platform with the trap door buttons on it. Stand next to the upper right button and look north. There's an eye on the wall. Shoot it with an arrow to make a chest appear next to the pedestals. Grab it for a Power Gem before time runs out. Go through the door and make your way to B6 as before.

Floor B6
Clear the floor as you did before. To the left of the stairs going is an alcove with an eye. Shoot it with an arrow and a chest will appear in the northeast. Grab the treasure map in the chest before time runs out.

Run south to the red door, hitting the floor switch along the way so you can actually reach it. I'd suggest drawing the hourglass first so you can nab the yellow jar inside. Run back out, then draw the Triforce in one stroke. See the section of the walkthrough on it if you're stuck. Once inside, a skeleton will create a yellow portal for you. This portal will allow you to automatically jump to this room from the entrance at the cost of however much time it took for you to reach this point. So if it took 3 minutes on the hourglass for you to come this far, then if you use this portal 3 minutes will be subtracted from your max time and you'll end up at this portal on B6. Very handy. Also, if you reach B6 the hard way with a faster time (say 2 minutes), then the portal will subtract 2 minutes instead. For the regular blue exit portal, exit and draw the hourglass on the door. Continue on, opening the Door of Courage.

Floor B7
Get on the moving platform that arrives and make sure you have your sword and shield out. Get on the next platform and face left. Your shield should block the arrows that fly at you. Move to the next platform and then onto the blue ground. This ground is odd in the respect that it will make sounds if you run across it. This sound will alert Phantoms, so as a general rule walk slowly on this when there are Phantoms nearby. When the Swift Phantom below is at the southwest corner of its patrol, run straight south and go down the stairs there.

Floor B8
When the phantom in front of you goes to the lower-left corner, run right and up. The exact middle of the wall hides an invisible path to the right. Find it by slowly walking northeast along the wall until you walk onto it. Mark this on your map so you don't forget where it is. Go up the stairs near you.

Floor B7
Look carefully at the moving platforms to your north. When the platform nearest you hits the northernmost point in its travel and the phantom near you turns right, shoot him in the back with an arrow, run over to where he is, and hit the switch. Run over to where the extinguished flames were, circling around the side of the pillar away from the Swift Phantom. Hopefully you'll get there in time to catch the platform. Face right when you're on the platform so you can block the arrows shot at you. Head left when the platform stops. Smash the yellow jar and open the chest for the round crystal. Watch some flames disappear on the right side of the room. When the platform comes back, cross over to the safe area with the crystal in tow. Drop off the crystal in the safe area and tap on the wooden pole to jump on it. Equip the boomerang and hit the switch to the southeast. Time this so the Swift Phantom is way in the south of the room. Get the chest that appears for a Power Gem. Run back and grab the round crystal. Make your way back to the stairs in the south. Hide in the red jar next to where the chest was if necessary. If you are spotted, drop the crystal and run to the nearest safe zone. If a phantom finds a crystal, he will pick it up. To retrieve the crystal, you must shoot the Phantom in the back with an arrow.

Floor B8
Run back across the invisible bridge and wait in the safe zone near the stairs until the regular phantom moves north and the swift phantom moves east from the corner to your northwest. Run up and east to the safe zone where the round pedestal lies. Run up to the room behind the spikes that retract and hit the floor switch to activate a wind vent. Go up the stairs and head south. Break the yellow pot with your boomerang, then jump to where the round crystal is. Pick it up. Wait for the regular phantom to head north. Go west, slightly south, then east to where the wind vent is. Ride the vent up and walk along the wall to the north. Jump off into the room behind the spikes and head down the stairs.

Floor B9
Put down the round crystal and open the chest for the triangle crystal. Go back upstairs with the triangle crystal in tow.

Floor B8
Run up the stairs and jump off the wall to the south when the Phantom passes you walking north. Go to the invisible bridge and cross it. Hide in the safe zone to the southeast until the phantom to the north turns left. Then run all the way up to the northeast safe zone or the red jar next to it. Wait for the swift phantom to turn south near you, then run over to the west. Drop the crystal and bomb the blocks surrounding the pedestal. Pick up the crystal and hide in the safe zone in front of the pedestal. Put the crystal in the pedestal. When the Phantom passes by you going left, run to the spikes that lowered and hit the switch inside. Run back to the triangle pedestal safe zone. Don't pick up the crystal. When the phantom passes by going right, run to the door that opened and go down the stairs.

Floor B9
The body next to you will go on about the sand in the hourglass suddenly going down. Look at the map and notice the four skulls. Approach the skull nearest you. Equip the boomerang. If you turn your back to the skull, the Poe will materialize. Hit it with the boomerang to kill it. It will drop 30 seconds of time - grab it. Kill the Poe to the south as well. Avoiding the swift phantom, kill the other two Poes as well. A chest will appear with a Wisdom Gem in it. Grab it. When the phantom is in the southwest corner of the room, bomb the blocks to your right and hide in the safe zone. When the phantom passes by, shoot it in the back with an arrow. Grab the square crystal it drops and put it in the square pedestal to the northwest. Grab the round crystal and head back up the stairs.

Floor B8
Go up the stairs and jump down. Place the round crystal in the pedestal. This will cause a chest to appear to the west. The invisible path to reach it goes north from the chest to the platform. It's fastest to run back downstairs and go up the other set of stairs in B9 and hide out in front of the triangle pedestal. So when the coast is clear, run up to the north platform and go south to the chest for a Courage Gem. Run back to the triangle pedestal, grab the triangle crystal, and run back downstairs.

Floor B9
Go to the safe zone in the middle north of the room. Drop off the triangle crystal on its pedestal and go up the western stairs to floor B8.

Floor B8
Grab the round crystal from its pedestal. Then, when it's safe, run around to the wind vent to the southeast. Run up the wall and jump off into the area with the stairs. Go down.

Floor B9
Drop off the round crystal in its pedestal in the middle north of the room. Then grab the square crystal and put it on the pedestal, too. Go through the door that opens. Open the chest at the top of the room for the Southeastern Sea chart. Step into the blue portal and return to the surface. Head to Linebeck's ship and leave.

Before progressing...
Go to Spirit Island. If you've been following this guide, you now have enough Wisdom Gems to upgrade the Spirit of Wisdom. Do so. The powered up Spirit of Wisdom increases your defense. I still prefer the Spirit of Power, though, but the decision is up to you. Head over to the Southeastern Sea.

The Southeastern Sea
Staying away from any islands for now, head to the middle of the sea. Sail around until you find a frog. Hit it and mark its signal on the sea chart. Then head to the southwestern island. Before you can dock at it, a cyclone will suck you up and throw you out to sea. A large flying monster with six eyes approaches. Linebeck handles the steering while you have to man the cannon. Shoot at the creature's eyes. If it launches a yellow energy ball, shoot that first. Each eye will take two hits. Dock at Goron Island.