You're taken back to Pirate Isle automatically following the narrow escape from Valua, and finally Fina admits the reason she's here: to travel around the world and collect the Moon Crystals hidden under each of the six moons.
The Crystals are purified moonstones, used many generations ago to control giant living weapons known as Gigas. At the height of the wars that encompassed the globe, a sudden and violent shower of moonstones known as the Rains Of Destruction wiped out a huge portion of the world's population and ended the Old World.
When you're given the Swashbuckler choice, say you'll help Fina in her mission. You'll then be introduced to Fina's companion (and primary weapon), Cupil, and she'll join your party. Be warned: she's only level 1 yet, so don't be too adventurous with her just yet. She'll level up quickly, however.
The First Moon Crystal
Head down into the Pirate Isle base, and you'll get an introduction to Chams, slivers of moonstones that Cupil eats, which will allow him to level up and become more effective in battle. The first one is about halfway across the first bridge towards Dyne's office.
Head all the way to the bottom of the underground base to find Vyse's parents standing next to the Little Jack. Speak to them both before going up the gangway into the ship. You'll then get a short cutscene discussing your best option for the first Moon Crystal to retrieve. Valua and Nasr are the closest, but trying to get back into Valua would be a bad idea just after breaking out of the Grand Fortress - so Nasr it is.
With the Harpoon Cannon, the Little Jack will now be able to break through the stone reefs that, so far, have been blocking your entry to certain parts of the map.
To Nasr
Leaving from Pirate Isle, follow the cloud barrier north past Shrine Island and then turn east. Go through the stone reef here and you'll find two Discoveries, the Silver Moon Pit and Sky Coral. Head back out through the same stone reef again and then go east again down through the tunnel in the rock to find yourself at Sailor's Island.
It's strongly advised that you go into Sailor's Island and pick up a few Repair Kits from the ship parts merchant; they'll come in extremely handy in a little while, and without a few you could find yourself in bother.
Turn South and follow the stone barrier partway along, then go through it to find the Nasrean desert. You'll get a short cutscene here with some information about Nasr and its arid conditions, as well as the first of Aika's many rumours about the lands in Arcadia. After the cutscene, keep following the reef's southern face until you come to an island.
On the southern tip of the island you'll find Maramba, but first there's a couple more Discoveries in the area. On the mountain range to the east you'll find the Topple Rock, and further on is the Wandering Lake; follow the larger land mass here as it curves to the south to find the Oasis and the Sandfalls on a circular island floating high up, and then finally land in Maramba.
Maramba
Aika, Fina and Vyse are standing on the docks, getting their first experiences of Nasr's heat, when the Little Jack reverses out of the port. Drachma's had enough babysitting; he's got an arcwhale to hunt down, and can't be wasting time looking for ancient crystals. For the moment, it looks like you're stuck in Maramba without a ship.
Right in front of you is a save point, and beyond that a building that serves as both ship parts merchant and the local Sailor's Guild. Sell any discoveries you've made, then head up the steps to the main Maramba entrance.
The weapons and armor merchant is the first store over on the left. Pick up a Nasr Cutlass and Ceramic armor for Vyse, and an Agile Robe for Fina. While the Nasrean Mail is an improvement over Aika's current equipment, don't buy it, as there's some better armor for her in a chest in the town.
Head all the way to the far end of the town and go up the small spiral ramp to the Dhabu stand - the one with the big pink animal standing beside it. Speak to the guy here to borrow one - luckily, it doesn't cost anything. Once you've mounted the Dhabu, walk over to the red poles on the rooftop beside the exercising man. Go through the door behind him and downstairs to get Nasr Combat Mail for Aika.
Back outside on your Dhabu, go down to the weapon merchant's roof tofind a chest containing a Slipara Box, then head back up towards the Dhabu rental spot and go through the big gates across the desert to the other part of the town.
On top of the largest building here is a chest containing 300 gold. Once you've got it, go to the Dhabu stand and dismount, then head over to the dried up well and go down the ladder.
Follow the corridor to the first fork and take a left, then follow that all the way along to find another ladder. Climb it and you'll find yourself in a ruined building back in the northern half of the town, where there's a chest containing a Moonberry.
Back down the ladder, go to the first fork again and head north. Use the switch on the left to move the door ahead of you, then go through it and turn left to get an Excavation Arm. Head ease along this northern-most corridor and turn right, then use the switch here to move more doors. Head through the west corridor that's now open and take the first turn to the south, then west again to find a third switch. Throw that and head all the way around to the north and then east to find a chest containing the incredibly useful Gem Of Fluidity. Go back down and throw the third switch, then go back to the second and use it again to clear your way out.
Back on the surface, head into the tavern then walk up to the dancer and talk to her. Agree to stay a while, and partway through the cutscene you'll get a Swashbuckler question - admit that you were staring. At the most inopportune moment, the dancer will come over and introduce herself: she's Bellena, and she's heard about your exploits at the Grand Fortress. She's greatly intereste in enemies of Valua, and offers to let you use her ship.
Once the cutscene's over, go out of the tavern and climb onto the Dhabu again, then head back to the north part of the city. Speak to the woman in the inn to get a special rate on your rooms for the night, thanks to Bellena's influcence.
Meanwhile, Drachma seems to be having second thoughts about leaving Vyse and company behind, but is trying his best to shake off any guilt. He catches a glimpse of another ship, sneaking around in the stone reefs nearby - it looks familiar to him, and he's got a bad feeling about what it means.
In the morning, go to the item store and stock up on healing items, then head down to the docks - saving at the inn or beside the ship if you feel the need. Walk over to Bellena to start another cutscene; Aika's suspicious of the dancer's motives, and is pretty blunt when asking what's in the trip for her. After Bellena tells the trio about her father's death in the Valua-Nasr War, you'll be given another Swashbuckler decision - choose "We'll do it!" as your response.
Head to the east, past where you found the Wandering Lake earlier and you'll see the Temple of Pyrnn soon - it technically counts as a Discovery too, which makes a nice bonus to any treasure you find inside.
The Temple is an impressive structure to say the least; four giant stone heads surround the walkway up to a huge pyramid. Bellena stays outside while the rest of your party resolves to find the Moon Crystal, as well as whatever other loot they can find.
Head up the steps in front of you, past the odd-looking pedestal, and up the huge staircase beyond. There's a save point at the top which you can use, then head through the big doors into the Temple itself.
The Temple of Pyrnn
Go down the corridor in front of you, and walk onto the barrel on the left. Keep pushing forward and Vyse will roll it across to the other side; this is a pretty important puzzle mechanic later in the dungeon. Go down another long slope and head along the walkway here until you come to a ladder, then climb down to the next level. Follow this ledge along to another ladder and climb down again, the take this path along to a doorway.
As you approach it, the camera angle will switch to show you the boulders rolling down it periodically. Needless to say, you want to avoid them, so wait until one has rolled past, then run down the slope. About halfway down, there's a door on the right (Vyse's left) marked by a set of torches on the wall.
Run up the slope all the way to find a chest - when you open it you'll be thrown into a battle against three Magma Tiki enemies, so patch anyone up who needs it first. Purple weapons and magic are most effective, and you'll be rewarded with the chest's contents, an Ancient Robe, when you defeat them. It's worth pointing out that all the chests in the Temple of Pyrnn are guarded by a trio of Magma Tikis.
Go back to the rolling boulder corridor and go all the way to the bottom when it's safe, and you'll come to the first barrel-rolling puzzle.
You'll need to roll the barrels at the sides into position first; they'll plug the first two holes, allowing the barrel at the end to roll over them into the third position. Plugging all three holes will unlock the door, but if you mess up and need to repeat the puzzle from the start, just leave the room and come back in.
Through the exit, go down another slope to find a chest with three Sacres Crystals inside. Take the exit to the right to find another chest, with a new boomerang for Aika in it, the Dancing Arc. Head all the way north for a third chest containing 774 gold.
From there, go south one room and then west twice to get a second barrel puzzle, which is the first to have colored barrels. Roll the red barrels in first, then the blues to unlock the door, which leads to another rolling boulder corridor. Again, halfway down there's a corridor to the right (Vyse's left), but this time there's also a Cham in an alcove opposite it. Once you've picked it up, go through the doorway opposite and follow the corridor all the way to find a chest containing a Moonberry.
Return to the boulder path and go down to the bottom, then through the door into a magma cavern. Follow the walkway through here all the way to the bottom - there's a chest on the middle level containing five Magic Droplets - and through the door.
Ignore the switch in front of you for now; head up the slope to the right and follow it left, all the way to the end. There's a chest here, guarded by Zivilyn Bane - a treasure hunter who's after the chest's contents. Bane is aligned to the Red moon, so as with most of the enemies in the Temple it's best to use Purple weapons and magic. Aika and Fina should use Crystales while Vyse attacks normally. Your reward for defeating him is the Rune of Ill Omen, which can be sold for a lot of gold when you get back to a town.
Head back along the walkway and go down the steps about halfway along to find a final rolling barrel puzzle, made more difficult by certain parts of the floor rising and falling as barrels drop into the holes.
First off, roll the barrel in the top left corner into the top middle hole. Next, move the bottom right barrel into the hole directly in front of it, and do the same with the bottom middle barrel. The middle left barrel can now be rolled all the way across the board to the hole directly in front of the red barrel, allowing the red barrel to be rolled into the central hole.
Head back down to the switch you saw earlier and use it; a torrent of water pours down and solidifies the lava, which means you can now walk across it to the save point. Equip Fina with the Gem of Fluidity you got from Maramba's underground tunnels - it will prevent her from being Petrified by the upcoming boss, and since she's likely to be the only one with the Risan spell so far, it's best to make sure she'll be able to move if its needed.
Make sure everyone's healed up with as close to full MP as you can manage, then save and head through the door.
Equip everyone with Purple weapons for this fight; the Red Moon-aligned Rokwyrm will take a lot more damage that way.
Use Aika to Focus, which will build SP for Vyse's Cutlass Fury move - or if you've learned it already, Pirate's Wrath. Cutlass Fury is a little better however; the time taken to build up the 21 SP for Pirate's Wrath leaves you open to attack a lot.
When you haven't got the SP for a special move, use Vyse to attack normally. While he won't do all that much damage, chipping away little bits of Rockwyrm's health will make things easier in the long run.
Fina should be used to heal the other party members; use items as much as possible to save SP for Vyse. Likewise, if you've got any Crystales boxes, which can be used to cast the spell without requiring MP or SP, they're hugely effective against this boss.
With the Rokwyrm defeated, run across its back to reach the other side of the lava pit and go through the door to find the first Moon Crystal.
Recumen
Back outside, save at the top of the steps before running down to meet Bellena again. Unfortunately, it seems you've all been duped: the Nasrean dancer is in fact Belleza, one of Valua's Admirals, in disguise. Ignoring Fina's pleas to the contrary, she places the Red Crystal in the pedestal, awakening the Red Gigas Recumen, and ordering it to destroy Vyse, Fina and Aika.
As the three run across the desert in an attempt to escape, the Gigas powers up an attack and fires - but a cannon impact throws off its aim at the last second, causing Recumen to miss its target. Drachma's come back, and is ready to help Vyse take down Recumen.
The main focus of your actions for this entire fight should be healing. Recumen's main attack, Red Ray, can cause upwards of 6,000 HP damage when it hits, but fortunately it takes a couple of rounds to charge it up. You can throw the Gigas off balance by firing on him just before it performs the attack (the red turn in the battle grid), but even that can be hit and miss.
This can be an extremely tough battle to win if you're low on Repair Kits and MP. Often, the Sacres spell's 8,000 HP repair can be more helpful than the 4,000 offered by a Repair Kit, but save it for just after the Red Ray.
After several rounds, Drachma will recommend a strategic retreat, while you formulate a better plan of attack. Accept his proposal and the battle with Recumen will end.
Fighting the Gigas itself doesn't seem to be very effective, but Fina points out that Recumen is only doing what it's told to by the person holding the Moon Crystal. Aika's figured a way out, and you'll get a Swashbuckler decision to back her up - the correct answer is "You mean, attack Belleza's ship?".
Belleza's ship is equipped with a number of nice new weapons you won't have faced before; Magic Cannons allow her to cast offensive magic on your ship, while Secondary Cannons and Torpedoes allow her to attack multiple times on the same turn.
For the first couple of rounds, have Vyse and Drachma attack, while Aika and Fina Focus, and heal when you need it. Keep your health as high as possible, occasionally the Lynx will hit you with three attacks at once, which can be devastating.
After a while you'll get a choice of attack plans, which will affect how the next couple of rounds go. Pick the second option, "Turn hard and try and catch her off guard" to get slightly easier proceedings. Keep the same strategy as before for the next few rounds, then you'll get another choice - pick "Set engines to full speed and get behind her".
For the next couple of rounds, the main aim should be Focusing to build up the 15 SP required for the Harpoon Cannon, although you can keep attacking occasionally. You'll get a third set of options after another couple of rounds; choose "Head straight upward!", and then use the Harpoon Cannon when you've got the clean shot to use it.
As a reward for beating Belleza, you'll get a Captain's Stripe and a 3" Blaster Secondary Cannon, as well as a Magic Cannon which will allow any Main Cannons equipped on the Little Jack to use offensive magic.
With the Lynx down, Belleza hands the Moon Crystal back to Vyse. The next step for the Moon Crystal search is Ixa'Taka, to the south under the Green Moon. You'll need a special type of engine to get through the tornadoes of South Ocean, but fortunately Belleza's ship has one that you can use. That'll leave her stranded in the desert, but none of your party seems particularly bothered by that idea.