Head into the Palace and drop off to the left side. Head left a screen and you will meet a regular Ball and Chain Trooper. Unfortunately, we do not have a Roc's Feather to use against this Trooper, making the battle much more difficult than as with previous incarnations. You can either choose to be aggressive and constantly run at the Trooper to try and attack him, or you can be reclusive and only attack every couple of seconds.
Defeat the Trooper in whichever way you choose, then enter the rectangular area above. Hit the black switch inside and many force gems will drop down. Collect them, then push the third block from the right down and the first block from the right down. Push the second block from the right to the right and head back right a screen.
Head right another screen and you'll find yet another Ball and Chain Trooper. Defeat this one as well, then break the rows of pots to the right. Create a Box formation and stand on the switches to reveal four chests on the platform above. Open them for another 355 force gems. Jump off the platform and head back left a screen then north a screen. Create a Box formation and step on the switch to cause many Stalfos and a regular Wizzrobe to appear. Defeat the Wizzrobe first (as it is most dangerous), then defeat the Stalfos as well.
Head north to the next screen and walk up the stairs. To the upper-left is a lever; use a Long formation to pull it, bringing out Boomerangs and Bows. Grab one of the Boomerangs and head left to the next screen. To south and below the wall are two switches. Use the Boomerang to hit both of them, then head back right a room and grab the Bow. Reenter the left room again and head down the stairs to the left.
To the right is a small gap with a long drop to the bottom. Near the bottom of the area is an eye switch along the right wall. To hit it, you will need to press A to prepare the Bow while standing up on the platform. Start falling down and attempt to shoot the eye before you hit the ground. This may take a few tries, but once you accomplish it, walk across the new path above that was created.
You'll find another gap here with an eye switch that is on the ceiling. Prepare another Bow shot facing upwards, then drop down into the gap and shoot the switch. Climb back up the ladder and head right across the gap, and collect the force gems. Look upwards and you'll see two holes in the ceiling; fire arrow shots into these to hit the two eye switches in the main room. Head back out to the main room.
Head north a room and you'll reach a maze. There are four eye switches in this room that need to be hit with the Bow. Unfortunately, they are often blocked by the maze barriers and can only be shot at from certain points in the room, making this rather difficult and annoying.
Follow the path to the right and head upwards when you first can. Take a left and head south around the middle two rows of spikes. Take the south path and face left, then shoot the eye switch along the left wall to activate it. Walk back up to the middle spikes and head left, then take the path south to the eye switch we just activated. Before you walk near the eye switch, stand along the south wall near the bottom-left corner and shoot upwards to the eye switch on the north wall, activating it.
Walk north until you are stopped by spikes, then head to the left. Follow the pathway to the top-left corner and open the chest for a Heart Container. Follow the path back to under the middle spikes, then walk upwards a tad so you are standing directly to the right of the top row of middle spikes. Shoot to the right and hit the third switch, then walk to the right a tad. Walk upwards a tad and head right, then face upwards and shoot the fourth eye switch. Walk upwards and follow the path to the top-right corner and open the chest for a big green force gem. Walk back left and upwards, then open the chests for a Moon Pearl and a Blue Bracelet. Exit to the screen to the south.
Head right a screen and use the Moon Pearl to create a Moon Gate to the south. Grab one of the Boomerangs to the right and walk around the Moon Gate, then enter the bottom-left door. Continue left to the next screen and push both blocks to the right to create a Moon Gate. Separate the Links and use one to enter the Dark World. Use the Link to grab one of the Links in the Light World, and move him onto the middle platform. Place him on the switch and a connecting platform will appear, along with the right door opening back up. Use the Dark World Link to hop into the other Moon Gate to the left, then have the Link sitting on the switch shoot the black switch to the left. Bring all the Links together on the left side and head up to the next room.
Open the two chests here for a small key and a Moon Pearl. Grab both of them, then head back south a room. Use the Moon Gates to reach the right side of the room, then head right another two rooms back to the main room of the dungeon. Head over to the right side and use the Moon Pearl to create a Moon Gate, then use the small key on the door nearby.
Grab one of the Pegasus Boots, then look to the right. Near the door is a Bomb, but it has a fuse on it. Grab one, then quickly enter the room next to it. Look along the upper wall and you'll see a cracked part near the middle. Use the Bomb to blow it up and enter the room. Give the Pegasus Boots to the Great Fairy and she will upgrade them to the Level 2 Pegasus Boots.
Head back south and walk to the right. You will need to use the Pegasus Boots to dash right, then dash up, then dash right, without hitting the ceiling above. This can be very difficult and may take a lot of time, so be patient. Once you make it, step on the switch and a big blue force gem will drop down. Use the Pegasus Boots to reach the other side, grab the force gem, and head up a screen.
Walk right and head down the stairs above. To the left is another gap. When you drop down you will need dash to the left and over to a chest in a small crop in the wall. Drop down, then dash when you see an opening in the wall to the left. Keep dashing until you reach the chest, then open it for a big blue force gem. Walk down to the right. When you drop off this area, you will need to quickly dash to the left. Do so, and climb up the stairs to get back out.
Open the two chests here for 40 force gems, then head down the next set of stairs. To reach the next ladder, you will need to dash more to the left. Soon though, you will reach a wall. Drop down for a little bit and you should land on a small outlet area. To the left is the ladder we need to reach, so you will need to drop down to the right, then quickly dash to the left and onto the ladder. This can be very difficult, so do your best to make it. Once you do, climb up the two ladders to get back out once again.
Open two more chests for some more force gems, then enter the second staircase. Walk a little bit down the ladder, then dash to the left until you reach some more ladders. Move over to the third ladder from the right and drop down. You should land on a chest; open it for a Blue Bracelet. Look down and you'll see a door in this small block. You will need to dash back over to the ladder to the right, then head back up until you reach the top. Dash to the left again along the ceiling and stop on the ladders from before. Walk over to the fourth ladder from the right and drop down, then move the control stick right when you reach the door. Enter it to get back out for the final time.
To make this room even more difficult, there are Blade Traps to the right moving across the gap. To make it across you will need to dash with the Pegasus Boots to the next small platform when the Blade Traps move out of the way. Dash to the right when the Blade Traps move up. A Wallmaster will appear, but he can be defeated with a single sword slash. Dash up to the next platform, then dash to the right when the Blade Traps move down. Turn to the right and dash across the gap when the Blade Traps move up.
Open the chest here for a Moon Pearl and 300 force gems. Now push the third block from the right and the first block from the right downwards, then push the second block from the right to the right. Head down and to the left, then back south a screen. Head left a screen and walk down into the lower level of this screen. Use the Moon Pearl to create a Moon Gate on the right side, then grab the Magic Hammer and walk through the door to the bottom-right.
Pound the two pegs here with the Hammer, then pound the floor to the right with a charged-up shot. This will bring spikes out of the floor, revealing the pathway you need to take. Continue to do this as you make your way across the path. Open the chest at the end for a big green force gem, then pound the last two pegs. Enter the door that opens to the south.
Jump off the platform and pound all the pegs except for the top-right, middle-left and bottom-middle. Walk on the pathway along the left wall and down to a Game Boy Advance screen. Walk down to the south end and follow the pathway until you exit the GBA screen. Continue to follow the pathway and take a right once you reenter the GBA screen. Open the chest in the main screen for a Heart Container. Reenter the GBA screen and head south, then right and back up. Open the chest at the end of the path for 50 force gems.
Head back out to the main screen and look to the right and you'll see a wall of blocks. Push the second block from the top and the fourth block from the top to the right, then push the third block from the top downwards. Enter the last pathway and open the last chest for the last Moon Pearl. Head back to the main screen of this Palace, the one with the three Moon Gates. Use the Moon Pearl on the bottom level of the room and grab the Bow.
You will need to have a Link enter each Moon Gate and step on the switch in each area of the Dark World. Make sure to open the chests for more force gems as well. Once you have a Link on each switch, bring them together back in the main room and head north to the next room.
There are two Hinox in this room and many spinners. Take your time here as there is only a small amount of room to move around in, and these Hinox are aggressive and take many hits to defeat. Grab the small key and head up to the next screen.
There are three Gohmas on this screen across the gap. Defeat them with the Bow like before. I'd recommend focusing on one Gohma at a time, so you don't have multiple Gohmas firing three fireballs at once. Once you defeat them head right a room.
Break the pots at the top of screen and hop in the hole under one of them. Open the chest to the left for a big green force gem, then climb up the ladder to the right and hop into the cannon. Shoot out of this area and hold down on the control stick, then dive into the gray platform in the middle of the screen. This will flip it over, allowing you to reach a new area.
Head to the right and separate the Links. Use one Link to throw another across the gap, then connect the platforms. Climb up the ladder and throw another Link across another gap, then connect the platforms. Continue to do this across the platforms and drop down along the wall to the right. Dive into the gray blocks below and open the chest for 200 force gems. Throw another Link across this gap and open the chest here for a small key. Climb up the tall ladder and exit this screen.
Head left a screen and use the small key on the small door along the left wall. Use the Bomb in here to break the blocks to the south, then open the chest for a Heart Container. Use another Bomb to break the blocks above, then use two bombs to break blocks on both sides of the pathway above. Grab another Bomb, then walk back outside and throw it across the gap. This should bomb open the left wall, revealing an entrance to the other side.
Walk back inside the wall and head up the pathway. Step on the switch to the left and the door outside will open. Head right and walk down the pathway, then exit the wall area. Head up to the next room and break the pots for some more force gems. Break the final eye barriers and head up to face the Palace boss: Vaati.
This is it, the semi-final battle between the evil mastermind Vaati and the Link(s). The battle with Vaati is actually fairly simple - especially the first part of it. Vaati will circle around the room with a vortex of wind beneath him. As long as you run away and stay away from him you won't take any damage, making him rarely harm you. Located around the room are four bombs that you can pick up. Pick up one of them and throw it into Vaati's vortex. It will climb higher and higher and eventually hit Vaati, damaging him and dropping force gems. Collect the force gems, then continue this process to complete the first stage.
After being hit three times Vaati will momentarily disappear, then reappear without his vortex. Hop down into the hole in the middle of the room and you'll land in a cannon. The goal is to shoot out of the cannon and sword dive into Vaati once you reappear on the main screen. Wait until he goes near the middle square gap and then shoot out of the cannon. Move the Links so they are above Vaati, then dive into him. If you get it right you should hit him, damaging him further and dropping more force gems.
Vaati will dive underground. Drop down below and use the ladders and platforms to reach wherever Vaati is floating around. Attack him with the sword and soon he will fly back up to the main room. Follow him back up using the right side ladder, then jump into the cannon again via the middle square gap. You will need to use the cannon again to jump dive into Vaati, although it is more difficult this time. Vaati will now avoid the middle gap more often, making it more difficult to hit him. Along with this, he will create a ring of orbs around him that will shoot across the screen after a couple of seconds. You can avoid this by jumping into the underground. Once Vaati floats over the gap, jump out of the cannon and attack him like before. Continue to do this until he is defeated.
And that's it! Vaati is finally defeated. The Links will walk outside in pure glory, until the Palace of Winds starts crumbling down. The real final boss Ganon will then appear with words on screen, waiting for the Heroes to reach him. After escaping to the Tower of Winds, Princess Zelda will realize that there is more trouble afoot. This will start a lengthy part of the game where you will need to escape the Tower of Winds by slowly climbing down it. This can be rather annoying, as Princess Zelda will have to climb down each and every ladder to get to the floor, wasting a lot of time.
Head down to the next screen via the stairs to the right. Drop down to the ground level and wait for Zelda to catch up, then walk down with her to the next level. Walk down the stairs and defeat the Stalfos in the middle of the screen, then enter the door here. Use a Cross formation to hit the four switches in this room, then head back out. Climb up to the chest in the top-right corner and open it for a big blue force gem. Climb down the stairs and defeat some more Stalfos, then head to the floor of this screen. Defeat some Castle Guards that appear, then head to the next screen.
Drop down to the bottom-left and open the chest for some more force gems. Climb up the ladder to the right and use a Link to throw another across this gap. Break the pot here and step on the switch to create a ladder for Zelda, then open the chest for a big green force gem. Bring the Links together and drop down to the floor, then defeat some more enemies. Head south to the next screen.
Drop down in the gap to the right then walk right a little bit and enter the door here. Grab one of the Roc's Feathers in this room and head back out to the main room. Climb up the ladder to the left and use the Roc's Feather to jump across the platforms near the ceiling. Enter the door at the end and hit the switch to reveal two chests. Open them for 100 force gems and a Blue Bracelet. Head back out.
Head down to the floor and enter the door at the bottom-left corner. Open the chest for a big red force gem, then head up the stairs. Take the right path and exit back to the main screen. Break the pots to the right to create another path for Princess Zelda. Drop down off this path to the left and you should land on a block floating in the air. Jump onto another block to the right and step on another switch to complete Zelda's path. Defeat the enemies that appear surrounding Zelda, then head down the ladders to the bottom-right.
The next pathway is very straightforward. Follow the path and grab the Bow, then use it to kill the two Gohmas. Grab the Roc's Feather again and jump up to the chest along the right wall. Open it for the final big green force gem. Follow the pathway to the bottom-left corner and a Ball and Chain Trooper will appear. I would suggest being aggressive with this one, as it won't have a chance to attack. Once you defeat it, continue and you'll reach the bottom of the Tower.
The floor will crumble below the Links and Zelda, dropping them to a lower level of the Tower. The dark cloud will appear from before, capturing Princess Zelda and taking her away. Ganon will appear out of the cloud, ready to fight. This is the final boss of the game and the true dark power: Ganon.
The first phase of this battle is actually rather simplistic. At its core, it simply involves hitting Ganon with the sword hundreds of times. You can make this easier and faster by creating a Wide formation and using the Roc's Feather to jump dive into Ganon, multiplying the damage. If you can't accomplish this, you can always just use the Wide formation and attack with four Links at once.
Ganon has a few attacks, though most are fairly easy to dodge. The first is a Lightning attack. Ganon will shoot Lightning out of the Trident to four different points in the room. The four points are usually near each other, so you can move to the other side of the room to dodge it. After taking enough hits, Ganon will also throw his Trident around the room, producing a blue flame that will damage you. This can also be fairly easy to dodge as well, and you can once again move to the other side of the room. At times, a Moon Gate will also appear on the floor. You can enter it and defeat the Stalfos here that would normally attack you in the Light World. Defeat the Big Dark Stalfos as well and no other enemies will attack you.
After taking enough hits, Ganon will disappear for a little while. Princess Zelda will reappear, and will produce a Light Orb. To finish Ganon off, we will need to use the Bow and shoot a Light Orb into Ganon. Unfortunately, the Light Orb takes a while to charge, and Ganon won't simply wait around for it to do so. We will need to deflect Ganon's attacks back at him to protect Zelda while the Orb charges.
Once Ganon reappears, create a Wide formation. Stand in front of Princess Zelda and move where she does, constantly standing in front of her. When Ganon sends out an orb attack, deflect whichever orbs will hit Princess Zelda back at him. Continue to do this until the orb charges and Ganon will be temporarily stunned. The Light Orb will start to circle around him, so use the Bow to shoot the Light Orb into him. Once you do this, Princess Zelda and the other Maidens will use their powers to seal Ganon within the Four Sword. With this, the game is completed and Hyrule is saved! Congratulations on beating the game!