Back on Flammie, you'll need to fly in search of a giant land mass that appears to be mostly submerged in the ocean. Except that the very center of it has a building sticking out of the water. Land Flammie on this building. You will land directly in front of the Tree Palace. There's nothing to find by exploring the area around you, so step inside.
Inside, you'll find the Emperor waiting with two of his henchmen. He announces that he's going to raise the ancient continent by breaking all of the seals, and he only has one more to break. Then Sheex, the Dark Stalker from Tasnica, will volunteer to defeat you. Then he transforms into a beast.
This boss can be quite challenging. It starts off the battle casting Wall, and it will never wear off, so casting magic against it is not an option. On top of that, it can cast magic at you and it does so quite rapidly. It primarily casts Burst and Sleep Flower, and it will typically cast several spell in a row, back to back. This is challenging for two reason. First, because Burst will cause a good amount of damage, and second because the monster is generally invulnerable when it's in the middle of casting. The next challenge is hitting it correctly. Because the central body hovers off the floor a bit, you have to be standing the right distance away from it for your attacks to land. Too high or too low, and they will miss. Aegagropilon can damage you simply by touching you, even if you happen to walk into it. It alternates between the slower spell casting form, and jumping in to the air before landing back down as a simple ball. This ball will roll around the room knocking into any player that gets in its way, before flying back up and returning to his previous form. Do your best to attack from a safe distance, and land as many hits as you can while it's vulnerable between its own attacks. It has a good number of hit points, and charged attacks will be best.
Upon defeating Sheex, you will obtain a Spear's Orb. Then head to the left and down to find the stairs that lead to the seed on the altar. Run to the seed and try to use your weapon on it, but you will find that the seed is melting. Dryad the tree spirit will appear and explain that the seals have all been broken, and the continent will rise. Dryad is prepared to be destroyed with the palace, but the Sprite convinces her to help the team instead. You will gain Dryad's powers.
After summoning Flammie, you view the situation from the air. The continent does indeed rise out of the ocean. Land back down before the Tree Palace. You'll find that the outside is now crawling with enemies. Jema is walking about nearby. Speak with him, and he'll explain that he brought troops to fight the Empire. The Emperor is trying to reach a city beneath the palace, and you must use the Mana Sword to stop him. If you step inside the palace, you will find that you can't proceed that way. You'll need to explore the outside.
Start making your way down the side of the Tree Palace, which now resembles a pyramid. Along the way, you'll encounter Dark Knights, Shape Shifters, and Metal Crawlers. Many enemies will cast Wall, so be careful who you attack with magic. Climb down the stairs until you reach the bottom. Both staircases lead to pools of water, but the right one deposits you in a dead-end, so use the left staircase. Around the bottom, other enemies will appear like Dinofish and Steelpions. Follow the pool of water to the left and up until you reach a staircase that leads underground.
You will appear in a small room. There are a couple of Steelpions to fight. In order to clear away the small objects in the ground that block you, you must use the axe. Clear them away to get access to the yellow creature that will boost you up to the next floor. There's a chest to the right of falling water. Approach from the top of the room as the falling water will push you back down to the floor below if you're not careful. Inside the chest is a Boomerang's Orb. Collect it and return to the door on the left.
In the next room, you'll need to use the axe to clear away all the bumps in the floor that prevent you from proceeding. A trail of gray bumps lead to a tile which, if stepped on, will reset the bumps. Heading to the left will lead you past the bottom of two waterfalls to a dead-end. Instead, explore up. You'll have to fight your way past some Metal Crawlers and Steelpions. Beware of Kimono Wizards. They fly in the air, so they're not easy to hit, and they summon Metal Crawlers. They are susceptible to Gnome magic, however. Near the top of the room, you will also encounter Basilisks. They can summon Eggitrices.
When you reach the top, start running to the left. You will eventually reach the top of a waterfall, and the force of the water will send you down. You can hold to slow down the rate that you drop, but you can't overcome it. Halfway down to the bottom, you should see a switch on the left. Try to hit it with your weapon as you drop. Doing so will cause the waterfall to cease, and you can run back up and continue left. If you miss it, you'll be driven to the bottom of the room, and you'll need to climb back up the right side again.
Assuming you were successful, run back up to the top and continue left. Drop down the next waterfall (it won't take you to the bottom) and then prepare for another trip down the next waterfall. This time, it will look like there are two switches on the left, but the real one is on the right. Hit it as you go down to stop the water, and run back up. Continue all the way to the left for the exit. Be sure to heal up before you enter the next room.
Hydra is a dragon with two heads that swing about independently. He is extremely difficult to hit without charging up your weapons. If you run a quick Anaylzer spell on him, you'll learn he's afraid of Salamando. Have both the Sprite and the Girl cast fire magic on him as much as possible, but watch the Girl's magic points, and make sure you leave enough to heal any damage. As Hydra takes more damage, one or both heads will fall away, but they will regenerate. This has no bearing on Hydra's health, just his ability to attack you. Keep cast fire magic until Hydra is defeated.
One destroyed, you will obtain a Whip's Orb. Then you will rush into the next room where you will find the Emperor. Fanha wants to engage you, but the Emperor decides to leave you to face your fate in the Mana Fortress, and leaves. Follow them up to the next room, and then continue past the Kimono Wizard and Metal Crawlers to the flight of stairs beyond. Continue on into the next room, and head to the right. Make your way down to the door at the bottom.
In the next room, fight your way past Metal Crawlers and Captain Ducks. Head to the right, where you'll actually find two escalators. The left one is going up, and the right one goes down. But if you head straight down, you'll reach a door that has a clear barrier in it that you can't pass. Along the left wall of the up escalator is a secret passage that leads to a switch. Step on this switch to open the barrier below, and return. Watch out for the Fierce Heads that patrol the area. Move down to the bottom of the room and run to the right.
Midway through, you'll pass a doorway (marked C on the map). Enter through it, and you'll actually reach a bit of a rest area. Inside, Krissie and another resistance member are waiting to let you know that they'll secure the area. One of the resistance member will tell you about red, blue, yellow and green but he has no clue what this is for. Speak with Krissie to restore your health (but not your magic). You'll even find Watts standing by to upgrade any weapons you collected orbs for. When you're done return to the room below, and continue to the right. Follow the hallway as it bends up and back to the left a bit to the next room.
Follow the green path way to the left, as the path up leads to a dead-end. It will take you to another room where you'll find another escalator. There are no secret passages to find this time, just head up and watch out for the Fierce Heads at the top. After a short walk to the right, you must drop down a one-way path to the floor below, and then back up a small set of steps. If you keep going up, you may notice a switch tile that's currently unreachable. You'll have to head to the right instead.
This will force you to do another one-way drop. A bit further to the right, you'll notice another doorway with a barrier in it. A path to the right leads to a switch above another door with a barrier. Step on the switch and return to the previous barrier you saw. It should be gone, allowing you to head up. This will send you up along a path that follows the top to the right, and then down along the right side of the room. Eventually you drop down into an area with four light tiles on the floor. The top one is a switch, which will open the barrier on the door above (marked F on the map), allowing you to pass through.
In the next room, you'll have to head up around a pool and up a hallway to a path above that takes you to the left. Then head back down, fight your way past a Basilisk, and follow the path as it bends back to the left to a Captain Duck. Beyond the small set of steps, you'll find a Dark Stalker in front of four consoles, each with a different color glowing light. Below them is a door with a barrier. You can explore the path below, but if you go too far, you'll fall down a one-way drop and be back where you were when you entered the room from the four floor tiles.
To advance, you need to figure out what order to press the console colors in. The resistance member in the room with Krissie had mentioned it if you spoke to them. Otherwise, this is purely guesswork, though there's no penalty for getting it wrong. You'll know you figured out the right color when it lights up and stays that way until you make a wrong guess. If you guess wrong, simply keep trying. Ultimately, the correct order is: red, blue, yellow, green. Once pressed, the barrier to the door below (marked G on the map) will open.
Pass through the doorway, and follow the path you're on as it goes left, down, and back to the right. This will lead you to the switch you could see before, but could not reach. Step on it now, and you'll hear the sound of something opening. The only doorway that you couldn't pass through was the barrier below a switch you pressed. Fall down the one-way drop and head to the right. You should eventually return to the switch, and the barrier on the door below will be gone. Head down and follow the path as it leads to another pair of escalators.
Head down the escalators and into the room below. Watch out for the Dark Stalkers in here, and head to the right. You'll need to pass through what appear to be a bunch of turnstiles. Beyond them, you'll actually find a train! The only open door to this train can be found on the left (marked I one the map). Step inside.
You'll now be traveling inside the train. You must make your way from the back of the train to the front. Along the way, you'll encounter numerous Ghouls. At the very front of the train, it appears as though an Eggplant Man is the conductor. Once you reach the front, step out of the train through the door at the bottom. Some Shape Shifters will be waiting for you outside. Run down in the new station, past some turnstiles, and fight your way past some Dark Stalkers. There will be Captain Ducks waiting by the exit. There are two structures here, and you must pass through the right one to activate a switch that lets you leave through the door below.
Out of the station, head to the right and fall down a series of one-way drops (the path lets you circle back around on the left side.) Continue down the left side to reach a door. You'll encounter the Scorpion Army again. This time, they'll seem to know who you really are. They decide to try and take your sword from you by summoning a robot they built.
Boss: Kettle Kin
This boss battle is similar to the previous fight you had with a Scorpion Army robot, only this one is capable of doing some serious damage. It stretches its arms out, and spins its hammers around in a circle. Anyone caught in the swing will get quite hurt, and has the potential of getting knocked unconscious for a short while. The robot is also very fond of casting Lucid Barrier on itself, which makes it extremely hard to hit. As a result, you're better off casting magic on it, although it's not particularly weak to any one type of magic. Be sure to keep your magic points up with Faerie Walnuts, and have the Girl focus on healing.
Once it's destroyed, you will obtain a Bow's Orb. Then the Scorpion Army will run away. Exit through the top of the room, and you'll find yourself back outside around the Tree Palace area. Return to it by heading to the left. Continue past the first set of steps, and you'll see a door between two flights. Pass through the door to reach your next destination.