Story missions are obtained from the Outland Count in the Mark Grand Court. You get new ones as the story progresses.
Head to the Old Forest Mine to the west and find an Iridescent Ore. Bring it to me, and I'll officially make you Tharsis explorers.
This is the first mission and it's simple as first missions usually are. Unlike other games you start in a mini stratum or Cave instead of the first main stratum and you also are not required to fully map out the Old Forest Mine. Just getting the ore will complete the mission.
The ore is located in A2 and you'll have to dodge some Nomad Baboons as two of them circle around the ore you need to collect. Once you get it go back and get your reward from the count which includes your own Skyship which you get to name yourself.
We now know that the lower level of the Lush Woodlands is held by a beast with red fur. You must eliminate this grave threat.
You get this mission shortly after finishing exploring the B1F of the Lush Woodlands. At the end of the B2F you'll fight a Bloodbear. After getting it's HP down to around half it'll run away to the B3F. Even if you go back to the Inn it'll still be wounded. Upon the Bloodbear's defeat you soon learn that there is a bigger beast out there. At the end of the floor you'll encounter the boss Berserker King. Make sure not to try and fight it head on. When you defeat it you'll get the Ancient Tablet key item as well as access to a new land.
A cordial relationship with the Vessels of the Misty Ravine would be most desirable. See that their Medium gets my letter, won't you?
You get this mission after your initial encounter with the Vessels in the Misty Ravine. Go back to where you met them and you'll learn that the Medium has been kidnapped. At B3F of the Misty Ravine you can ask for Wufan's help. At the end of the floor lies the boss Hollow Queen. Defeat it and you'll get the Second Tablet in addition to gaining access to a new land. Wufan will also give you the Circle Staff which will let you create your own Arcanist.
The Sentinel's face extinction due to this plague, and only the Titan's Heart can cure them. Find it and deliver it to them.
After meeting Kibagami and Sentinels in the Golden Lair, you'll get this mission. You'll have to fight Kibagami before you can help the Sentinels however. After you beat him you'll have to make your way to the bottom floor and can get Kibagami to help you much like the last mission. At the end you'll find the boss, the Boiling Lizard. In order to make the fight easier it's recommended to take out the stack of scales in the back but you'll have to slowly make your way to it. You should also carry some ice stakes with you during the fight. After beating the boss you get the Titan's Heart as well as the Battle Goblet which will let you make a Bushi with. But there's no Tablet to be found...
The self-styled Empire that has kidnapped the Medium would like to meet with me. Please act as my escorts on the Journey
This brief mission is obtained right after some surprising events unfold. Just go to the South Sanctuary after accepting the mission. Be sure to be healed up and you'll end up fighting Logre not too soon after you arrive there. After he flees you'll return the Court with the Count.
The Empire's aims are loathsome and our negotiations have broken off. I need you to rescue the Medium and stop the Empire.
You get this immediately after finishing the last. Before you can get to where you need for this mission you need to get the Black Flame at the Windy Archive. Once you have it you still won't be able to make it there as several of the Empire's skyships guard the stratum. Luckily Kirjonen and Wiglaf are willing to help you get in. After you get the Skyships distracted you can finally make your way into the Echoing Library. Early in B3F you'll have to fight Logre again but he won't run away this time. After his defeat you can choose to ask for his help. You'll fight the Cradle Guardian at the end of the stratum and after defeating him you'll get the Drive Blade Key with which you can make an Imperial.
The Imperial Prince took the Medium and absconded, but this is not over. Head him off in the depths of Yggdrasil!
The final mission. Enter the hole where Yggdrasil was to enter the Forgotten Capital. You won't be able to see much of it until you go through a portal off the the left where the big door is. From there you'll get to explore new sections of the bottom of the previous strata. You'll need to find the big tablets at the end of each section and activate them. After this rather long detour you can finally explore the Forgotten Capital. There's only one floor and at the end of it is Baldur himself who then becomes Cursed Prince and fights you. When you beat him Yggdrasil itself will emerge from the stratum and will stand there ready for you to fight him as the final boss, Heavenbringer.
Once you've watched the credits, save and load clear data, then report to the Count to finish the mission.
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