Now head back to where you and The Girl discovered that you couldn't move on without an Axe and use your newfound weapon to hack down the trees, and you can continue. After warping a couple more times you'll end up at Elinee's castle. There are Werewolves here. Continue around the path and head inside.
Inside there are mostly Eye Spies, with a couple of Haunted Chairs. The Eye Spies can hit you with a beam that shrinks creatures. Once you reach the room with a pair of Werewolves inside, you'll see a switch that seems to do nothing. Go down from there to find the Pandoran soldiers you saw in front of the Water Palace imprisoned. Release them, but you'll find they're all zombified like the people in Pandora. However, one soldier tells you that the switch needs to be stepped on by 3 people at a time to reveal the path forward. You also find Neko here, who was caught as well.
The next room has 3 doors, the left and right just have some enemies in them. The middle is a room with 2 Haunted Chairs on a staircase, this is where Elinee is. Talk to her and she disappears. Go out the back door to follow her. She has Dyluck, but sends him off to someone named Thanatos, the leader of a now not so secret organization that's going to take down the Pandoran kingdom. He and Elinee have been turning the people to be zombie-like and he's set to storm the castle from the ruins to the south of Pandora. Elinee disappears and sicks her Spiked Tiger on you before you can do anything to her though.
Spikey is pretty cheap. He knocks you unconscious, lights you on fire, and can even jump on the high pedestals to the right and left of the main area to avoid your close ranged attacks. After defeating Spikey, Elinee will be waiting in the previous room. She changes into an innocent looking old woman, and explains that she got some 'magical herbs' from Thanatos that made her evil. Anyways, she says she won't be any trouble from now on, and even gives you the Whip. She says that she sent Dyluck to the ruins to the south of Pandora and that to break the seal on the palace under the dwarven village you need the magic of ice, but she can't break it herself anymore. With the whip you can access a hidden path from the Haunted Forest to the Water Palace.
Once you get outside the castle, The Girl is relieved that Dyluck is alive. Luka then contacts The Boy telepathically, telling him to hurry back to the Water Palace. As you go back through the forest, there's a small staircase that goes to a platform with a post on it, and a post opposite over a gap. The Whip can be used to pull your team over the gap and to a hidden teleporter that leads outside the Water Palace.
Returning to the Water Palace, Luka explains what's going on. She has a connection with the Mana Spirit of Water, Undine, and she can't feel her presence and thinks something is wrong. She asks you to go to the cave to the east of the Palace and check on her. Head back outside and go right at the bottom of the stairs outside to find the cave. There are a few Iffish outside they attack by spitting water at you, and as long as you don't let all of them hit you at once, you won't get trapped or anything.
A little ways in the cave you run into a small egg that hatches into a baby Tonpole. Once you do enough damage, he will 'evolve' into a full grown Biting Lizard. He doesn't move or attack all that fast, and he uses no magic other than cure water when he gets low on health. Upon defeating him you can go to the back of the cave to meet Undine. She gives you the last mana weapon, the Javelin, and she grants you the power to use magic. The Girl gains the ability to use Undine's healing and support magic, while The Sprite is able to use Undine's attack magic.
Returning to Luka tells you that Undine's magic can open the Earth Palace in the dwarf village, so head back there. Use Freeze on the orb, which cools the lava blocking your path, and you will be able to go inside the Earth Palace.
The Goblins in here can be a problem, as the Ma Goblins spawn more if you don't take care of them, and they have ranged attacks. When you get through the first set of doors, your way is blocked by a large torch. Head to the right and the left to find rooms with switches you step on. Once you've hit both the path will open. There are more Slimes in here that multiply, as well as the Chess Knights, which have really high evasion. Once you clear the first area the rest of the dungeon is linear. You'll have to cross a gap with the whip and fight more, but no branching paths or big surprises. Once you reach the stage area, you'll find Gnome, the Earth elemental. He and The Sprite get into a fight for a minute, and then there is an earthquake and a boss, the Fire Gigas, appears.
Fire Gigas can chain-cast some fire spells as well as move around the battlefield by splitting into multiple fire orbs to reform at a different location. The Fire Gigas is weak to spells like Freeze. Once you defeat the Fire Gigas, Gnome will grant The Girl his defensive and supportive magics and grant The Sprite use of his offensive spells. Once you seal the Earth Mana Seed, the Sprite will regain their memory, and he knows where he lives, in the Upper Land Forest. Before you go there however, you need to return to the Ruins south of Pandora to face Thanatos and rescue Jema.
When you return to Pandora, the city being much the same, fewer citizens roam the streets and those who still remain silent. Near the south exit of the town is a woman with blue hair. The Girl will recognize her as Phana but she disappears. Nearer to the Pandora Ruins you will again find the woman, Phana, again outside. Upon approaching, Phana will hit The Girl and tells her to leave her alone, and runs inside the ruins. The Girl pushes past the guards, allowing you to go inside the ruins.
Inside the ruins, the enemies have healing magic and incredibly high evasion, and you are almost forced to use magic to kill some of them. Many of the enemies are slower so the you could run past almost all of them. There's creepy music here. It's not that large of an area, and is farily linear, so you don't have to worry about getting lost. The first room has three doors, just go in the middle one, the other two doors hold small chambers used for silent meditations. When you reach the back, there will be a room with a lot of cultists, and you'll find Thanatos, Dyluck and Phana. Thanatos recognizes the Mana Sword and is surprised The Boy is the one who wields it. "Now, that it's interesting." He also says Dyluck had a strong spirit and was hard to drain of his energy, but that he's his slave now. When you move towards Thanatos to attack, he pulls the rug from under your feet, and the floor from under the rug, and drops you into a pit to fight a boss.
BOSS - Wall Face- An animate wall with a face on it. With three eyes, the player will need to think of a strategy and quick as the wall slowly begins to move, making the room smaller and pushing the party closer to an opposite wall made of spikes. If you close one eye by killing it, the center one might resurrect it, but not with a whole lot of health. The side eyes also heal the middle one a lot. If both side eyes are gone, the middle one will open permanently and then the wall starts moving. It's going to crush you against the bottom wall if you can't kill it in time. The center eye does not have any offensive attacks.
After the fight the party can easily climb out to the main room. Jema is in the ruins now, he and other resistance members ran Thanatos and his followers off. He tells you you need to visit the Water Palace as Luka needs to talk to you. If you return to Pandora Castle. The king will reward you now that the curse that fell on his people is lifted due to your intervention. He will have a soldier move out of the way so you can get to the treasury, which has a few treasure chests filled with Gold.
Returning to the Water Palace you will find Luka and she informs you the Water Seed has been stolen! Luka, informs you the waters have shown her that the Water Seed is deep underneath Gaia's Navel. Once you return to Gaia's Navel, and the Dwarven Village you will find a new hole in the middle of the town, with a rope the party can descend and find The Pirate's Ship.
Here you'll find the culprits, the Scorpion Gang. (Though there are only 3 of them...) They say they stole the seed to power a weapon of theirs and you're going to have to fight it. BOSS: Killroy, the Scorpion Gang's weapon. It overloads with the power from the Water Seed and is ineffective, so they switch to auxiliary power. Killroy is ultimately a crudely constructed robot and its attacks are strong but easily avoided. His hammers can shrink targets or stun you. Once Killroy is destroyed the Scorpion Gang will run away and you can retrieve the Water Seed undamaged.
Returning to the Water Palace you will find it being attacked by monsters. The Water Seed being removed had weakened a barrier around the Water Palace. Undine will send a thought through The Girl or The Sprite telling them to hurry to rescue Luka. When you go inside, there are more monsters. Near the atlar you will find Ghestar, one of the empire's generals. He uses Luka as leverage to get the Mana Seed. Clearly there is no other option but to hand over the Water Seed. Once Ghestar has the seed he breaks the seal and leaves you to fight his pet, Jabberwocky.
BOSS: -Jabberwocky- can cast poison cloud on your party and occasionally his attacks will knock you down, but he doesn't hit very hard, and doesn't move all that much due to being in a smaller space in the temple. Once Jabberwocky is defeated you can return to the Water Seed to return the Mana Seal, restoring the barrier. Luka, tells you to visit all the palaces around the world to get the mana seeds power, and to visit a sage Joch in the lofty mountains, he will help you as well.