After the Emperor breaks all of the Mana Seals, the sunken continent rises, making the underground city accessible.
Explore the Palace
The monsters in this area are very tough. If an enemy seems to always avoid your attacks, try casting Speed Down on it, and cast Speed Up on yourselves. You can also cast Balloon or Sleep Flower to temporarily prevent the enemy from avoiding your attacks. You can cast Flame Saber on your weapons to make your enemies become Engulfed for a while. You can try casting Change Form to transform your enemies into weaker enemies. If an enemy uses Wall, use Dispel Magic. MP Absorb will (eventually) stop your enemies from casting Wall and other spells.
The door near Jema just leads to a dead end, so go down the many stairs of the Grand Palace and walk west through the water until you reach some stairs going down. Use those stairs when you are ready.
In the first room, get past the Steelpion and walk across the water. Use the axe to cut away the purple things blocking your path. Step on the yellow creature to be thrown to the upper level. Go across the water while pressing up, then open the chest to get a Boomerang's Orb. Then cut through the purple and blue things to the left and go north through the door there.
Cut through the blue and purple things with the axe. Don't step on the switch: all it does is make the purple and blue things come back. Go north past that switch, then follow the path left. After you get past the Basilisks, walk into the waterfall while holding the up button. Stay next to the left wall, then hit the wall switch when you pass it. This will turn off the waterfall.
Go north again, then go left and into the waterfall. Press up while walking left past this waterfall.
Go into the third waterfall while holding the up button. Stay next to the right wall, then hit the switch when you pass it. When the waterfall is gone, go north and then west.
Now you have to fight a boss: Hydra. Have Primm and Popoi cast Salamando spells such as Exploder and Blaze Wall. After the battle, you get a Whip's Orb.
Go through the north door in Hydra's room. In the next room you will find a Kimono Wizard and two Metal Crawlers. Get past them and go down the stairs. Next you will find some Metal Crawlers and a Steelpion nearby. Go south. The exit is in the middle. Go south through it.
There are more Metal Crawlers in this room, and farther on you will encounter a Captain Duck. To the south, there is an up escalator and down escalator. Go down the one on the left that is going up, while pushing toward the left wall. You will find a secret path into a secret room. Step on the switch there. Now go east and go down the escalator. At the bottom you find a couple of Fierce Heads. Farther south, there is a Kimono Wizard. Go east and through a narrow wall. There is a Steelpion over here. There should be an open door in this area. Go in.
You find Watts and Krissie. You can forge your weapons with Watts, then talk to Krissie to be healed. Talk to the soldier in this room to learn the secret code: Red-Blue-Yellow-Green. Now leave the room.
Go east through the narrow wall. Follow the path and go through the door at the end. There is a Captain Duck here. Go left (there is a dead end to the right). Walk into the wall at the end of this path to go through a door.
There is another set of escalators here. In this area, there are tall ledges that only go one way. If you fall down one of these ledges, you can't go back up. Make sure not to fall down a ledge unless you are ready.
Go up the escalator, then go down the one-way ledge at the top. There is a Captain Duck and a Fierce Head in this area, and a Kimono Wizard to the north. Go east past a small pool of water and drop down the one-way ledge east of that pool. Notice that there is a path blocked by lasers to the north. Continue going east until you find a switch. Step on it. Go back to the west and then go north through the corridor that was blocked by the lasers. Follow the path, fighting monsters until you reach a one-way ledge. Go down the ledge, then step on the topmost tile to remove the lasers from the door. Go through.
The next area is a straightforward path. Just follow it until you reach the area with the colorful switches
on the wall. Hit the switches in the order of the code that you learned from the soldier:
Red-Blue-Yellow-Green. In other words, hit them in this order:
4 2 3 1
After you do that, the barrier south of the switches will open. Go through the door past the barrier that just opened.
Follow the path and then step on the switch. Fall down the one-way ledge just below that switch, then go east until you find a switch that you stepped on earlier. Go south from that switch and follow the path. You'll reach another set of escalators. Go down either one and go into the door at the bottom.
Go east and get past the Dark Stalkers, then go north past the Captain Duck. So the ancient city has a subway station.... Go west and enter the door of the subway train. Go east through the train, fighting Ghouls. You might encounter an Eggplant Man here as well. For a quick way through the train, just press A to run all the way east. At the east end of the train, go through the south door.
There are a couple of Shape Shifters just outside of the train. Go south until you reach a door blocked by lasers. Walk through the tops of the H-shaped buildings to remove the lasers. Go south through the exit.
Go east and then south down the one-way ledges. Follow the path and then go through the door at the end. The Scorpion Gang will send Kettle Kin to attack you.
Kettle Kin uses Lucid Barrier, which prevents weapon damage. Use Dispel Magic if it has cast Lucid Barrier, then use Magic Absorb to stop it from casting Lucid Barrier. At that point, attack it with weapons. It only has 1230 HP and 33 MP.
After the battle, you get a Bow's Orb.
Prepare for the Grand Palace
Now that you have defeated Kettle Kin, you can reach the entrance of the Grand Palace at the bottom of the tower. You can can Flammie to take you out of the area, then come back after you have healed up and prepared. When you are ready, go into the double doors at the base of the tower to enter the Grand Palace.