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Return To The Tower
A cutscene will show energy coursing along the Spirit Tracks from the Ocean Temple to the Tower of Spirits, and then the floating section of the tower that's below the topmost section will now be joined together. This will give us more floors to explore in the tower.
Now that we're back on the train, a new track has appeared that will help us get back to the Tower of Spirits faster. Plot a course using the new track and get the train rolling back to the tower. Here along this track, watch out for the pirate ships that will blast their cannonballs at you. Give them a good dose of iron right back at them with your cannon to sink them.
By now you may also have noticed a familiar face floating around the map screen: that of Beedle from The Wind Waker and Phantom Hourglass. He runs a shop that travels on a hot-air balloon. Travel near where his face icon is traveling around and give him a train whistle to get him to stop down so you can shop his wares. He's selling a Bomb Bag for 500 rupees, which you should have enough to pay for right around now. This will give you 10 bombs to start with, and you'll have other opportunities to increase your bomb bag size up to 30 bombs.
Tower of Spirits
Once you return to the ground floor room of the Tower of Spirits, go back up to the winding staircase, and then travel up the staircase to the new door that's opened up and you'll start your next search on Floor 13.
If you liked them in Phantom Hourglass, you'll love their return appearance in this game -- the Phantom Eyes! For the next few floors, you'll be dealing with these "eye spies" that patrol the floors and alert the Phantoms of our presence if one of them spots us. If one of these gets on you, it can also slow you up, requiring a quick rub with the stylus to break free. Phantom Eyes can be killed, but unlike their Phantom Hourglass counterparts, they can regenerate. Also making an unwelcome return in this game are the Warp Phantoms, which will when alerted teleport to our location very quickly, barely giving us time to escape.
On this floor there are two of the three Tears of Light we need to power up Link's sword for Zelda to put on Phantom armor again, and the third Tear is on the next floor. Before we get to the first Tear on the southeast section of this floor, go east and stand halfway between the lit torch and the unlit torch, then, while watching the movement of the Phantom in this area, use the Boomerang to strike the lit torch and then the unlit torch. A small chest will appear in the northeast section which will contain a small key we're going to need. Then carefully make your way into the Safe Zone where the Tear is, guarded by a Phantom Eye. This will instantly alert a Phantom to appear near this spot. Wait until it passes before proceeding to the northeast section, also watching for the Phantom Eye on patrol there. Head for the Safe Zone in that area where a switch orb is located and hit it. This will cause a bridge to appear crossing two platforms in the southwest section.
The second Tear is located in the northwest section, which will require some whip-swinging work to get there. First go up the stairs to the platform in the northeast section, then use the Whip to pull the sword of the middle fish's mouth and aim it into the fish mouth on the right. A small chest will appear in the southwest section of this floor across the bridge we've just opened up, which also contains a small key. Now proceed to the two posts on your left and whip-swing across to the next platform, then whip-swing again one post to the left, then two posts downward, then run to the right and whip-swing one post upward. While you're doing this, watch out for the Phantom Eye patrolling this area. There's also another Phantom Eye guarding the Tear in the Safe Zone there, but don't worry about that one: just get the Tear, wait for the Phantom it alerts to disappear, then make your way back to the northeast section with your whip-swinging.
Grab the small key that's in the chest, and open the locked door in the northeast section to go up the stairs to Floor 14.
Go south until you reach the hallway on your left, then go that way but stop before you reach the corner so you can hit the Phantom Eye with the Boomerang to stun it. Then continue to head west until you see two loops to the north of you. A Phantom Eye will move around in a circle in the west loop. Carefully make your way past it to the east loop, near where a Phantom is standing around guarding the last Tear of Light. Use the Boomerang to hit the wall near the Phantom so you can distract it long enough to scoot into the Safe Zone and grab the last Tear to power up your sword. Then wait for the Phantom to return to its spot and strike it from behind so Zelda can possess its armor. Now that Zelda has the form of a Warp Phantom, we can make her teleport to any place where a Phantom Eye appears.
To test this out, have Zelda teleport to where the Phantom Eye is inside a room behind a closed door in the southeast section of this floor and then guide her to press a floor button to open the door. Then guide Link over to the room (don't worry about the Phantom Eyes at this point; all they'll do here is slow you down) and go inside to open the treasure chest which contains some random treasure. Or you can just get Zelda to teleport to each of the Phantom Eyes along your way back to the staircase to take them out one by one.
Whatever you do, head back to the staircase to go back down to Floor 13.
Now that we have Zelda as a Phantom again, have her teleport into the area in the northwest section of this floor behind the closed door where the Phantom Eye is. Then have Link get the small key that's in the chest in the southwest section and open the locked door located there. Behind the locked door is a switch orb, and across from that in the area that Zelda is in is another switch orb. Both of these need to be hit at the same time, so guide Zelda over to the switch orb to strike it then switch back to Link to strike the other one at the same time. The closed door will now open, and you and Zelda can take the other staircase that goes back to Floor 14.
Head south from the staircase to the southwest section of this floor, letting Zelda deal with the blue Electric Chuchus that Link cannot slay. Then have Link cross over the patch of sand to your right and stand on the right floor button while Zelda stands on the left floor button. This will create a bridge for Zelda to cross over the sand (as a Phantom, her weight would cause her to sink). Then have Link go to the right past the room which the spikes are barring him from entering and stand on a metal platform with a circle on it. Then direct Zelda to enter the room and stand on the other metal platform with the circle. The platforms will cause Link and Zelda to swap locations with each other. With Link now inside the room, have him go over to where the two fish mouths are on the left and pull the sword out of the left fish's mouth and then aim it into the right fish's mouth. This will cause the door on your right to open. Direct Zelda to reenter the room so you can both go through the door and up the staircase to Floor 15.
From the room that you start in, have Zelda go past the spikes into a corridor going to the left and then go down and to the right where she stands on a metal platform with a triangle on it. Then have Link stand on a similar platform right across from her to swap places. Then go right and then north and then to the left, avoiding the Electric Chuchus and the Zora Warrior, until you come to a room with two floor buttons that need weight to keep them pressed down. Push the block in that room over to the button on the right to keep it pressed down. Then have Link stand on a nearby metal platform with a square on it and then have Zelda stand on a similar nearby platform to swap places again. Then direct Zelda to stand on the other floor button to keep it pressed down. The spikes barring the door to your right are now disarmed. Then have Link and Zelda gather in the same room where the Zora Warrior is and use the same strategy of Zelda confronting it head-on while you strike it from behind to defeat it. North of that room is a big door that requires both Link and Zelda to push it open together. Past that door is a room with a chest that contains a small key in it.
Grab that key and head back into the center room with Zelda following you. This time, take the winding passageway to the left where you'll be stopped by a gap. Have Zelda warp to the Phantom Eye on the other side while you hit the switch orb on the other side with the Boomerang. This will cause a bridge to appear across a patch of sand for Zelda to cross. Then carefully direct her to cross the bridge and go all the way south and then east and then south across the spikes and then east again until she reaches a metal platform with a circle on it. Have Link stand on a similar platform across from her so the two of you can swap places. Then warp Zelda again back to the same Phantom Eye and this time direct her toward a floor button in an alcove southeast of the other two floor buttons to keep it pressed down. The spikes barring Link from going north will now be disarmed, allowing him access. Now have Zelda go before Link and repeatedly block the rolling boulders from hitting him so he can move north and then to the right where the two floor buttons are. Then have Link stand on one button and Zelda on the other to make a bridge appear crossing the gap to the right.
Now have Link go north across the sand patch and, before he gets sighted by the Phantom Eye, have him stun it with the Boomerang, then use the Whirlwind to blow it to the left across a patch of sand in the northwest corner room where the two floor buttons are. Then warp Zelda over to where the Phantom Eye is and have her stand on one button while Link stands on the other. A door blocking a locked door in a passageway heading north to a staircase will open. Now warp Zelda over to the Phantom Eye in that passageway and have Link go over into that passageway to summon her to follow him as you both go to the staircase that leads to Floor 16.
Here we have a light-up-the-tiles puzzle that requires Zelda to copy the movements of the Phantom moving around in the east side. Transport Zelda to the west side via the Phantom Eye located there and place her at the green tile in the upper left corner. Then direct her to travel south to the lower left corner, then northeast to the upper right corner, then west to the upper left corner, then southeast to the red tile in the lower right corner. This will open a door near the south end. Then have her walk through the door of spikes so she can rejoin you and go through the now-opened door to the staircase that leads to Floor 17.
Finally, we have the fourth Rail Map! This will open up a track in the Snow Realm that will lead you to the Fire Realm, the new area we're going to explore. However, just as Link and Zelda are giving each other high-fives for their achievement, Chancellor Cole's right-hand man Byrne shows up to unleash his power upon the two adventurers. But Anjean also shows up to protect them from Byrne. Apparently Anjean and Byrne had a history together as teacher and student, but Byrne decided to go his own way to become more powerful than the spirits. Anjean has Link and Zelda transported to the ground floor of the Tower of Spirits while she deals with her former student.