Raven cleans up nice.

So the explosion out side was some how connected to using a 1000 year old telepotert for the first time (it's never explained), and now Estelle and Raven are missing. The party tracks the transporter signal to that odd town they woke up in after passing out in the desert, only now there is no town. It looks like the town has been abandoned for a long time and been reclaimed by the desert, did the party time skip or somethign when it visited there? They also see there the guy who kept saving them, but he then leave on a dragon. Before they can look around much the head of all the knights shows up and basically says that he's the big bad that's been after the crystals, manipulating the corrupt nobles, making artificial orbs, and kidnapped Estelle. He then leaves Flynn to finish off the party, since all the knights have to follow him. Flynn admits that he knew the guy was behind it all but thought the reasons were right (though he didn't know what they were) but now he sees the his commander is just insane, and allows Yuri to run off and save Estelle.

They find the commander and Estelle (trapped in a magic bubble) in an old temple, and he is using Estelle as a weapon. While chasing after them they meet up again with the guy who keeps saving them, and he give them a magic sword that can dispel the magic in the air (it's also the symbol of the emperor). They catch up with the the commander just after he had killed another talking monster for it's crystal. Having lost control of the knights Flynn leads, he then orders the leader of the group of knights who keep trying to arrest Yuri to finish the job. It turns out that Knight is none other than Raven! Raven has been a double agent all along, establishing himself into the guilds and then keeping an eye on the party. Now he has his hair cut, mostly clean shaven and wearing fancy gold armor. The party has to fight him, and after they win it's revealed that 10 years ago Raven died in the war against the talking monsters, but the commander used an artificial magic orb to bring him back to life, so Raven had to do what he said or else the orb would be taken away. The commander, not wanting to take any chances, tried to blow up the temple with the giant walking fortress before finding out the result of the battle. Raven uses the power of his orb to hold up the ceiling long enough for the others to escape and remains inside as the place collapses.

The party chases after the giant waling fortress with the whale dragon as it walks across the ocean, and manages to find a small section of it to land on that isn't trying to kill them. Turns out that the section is clear because Raven not only managed to get out of the collapsing temple but also get to the fortress before a freaking flying whale! Also he's back to his old appearance, even with longer hair and stubble some how. After a lot of fight and some odd puzzle solving, the party make it's way to the control room, only to find that crazy assassin again! After the 4th time fighting the guy the controls are damaged and the giant main cannon is on overload. When the party can't slow it down in time, Flynn shows up with half the royal navy and manages to push the fortress enough so that the cannon misses the capital and just blows up a big chunk of the landscape.

The Party then gets back on the whale dragon and races after Estelle and the commander, who have now reached the capital. In a great anime cut-scene the Yuri tries to jump off the dragon-whale to reach Estelle, but the commander uses Estelle's power to blast him back. Then right after Estelle pleads for the others to kill her to stop the commander, he uses her at full force and blasts away the dragon. They all crash land and are injured, including the dragon who has to fly off to heal for a while, and then limp back to the port town to recover. Due to the huge hole in the land the cannon caused there is no direct way to to get to the capital, and flying is now not an option either. So I save the game just when the party has to travel across the northern ice flows to reach the capital from the back.