All story missions are received from Senator Flowdia at the Via Senatus after reaching a certain floor or after being prompted to return to her to accept a mission. Usually you are unable to proceed any further in the Labyrinth until you have completed the current mission.
Prelude to the ForestEdit
Anyone daring to survive as an explorer here in Armoroad must first pass the Senatus's official quest. You have been tasked with creating a map of the first floor.
This is the first mission you will receive before you are even able to enter the Labyrinth. It is fairly straightforward, and you only have to map a bit more than half of B1F. There will be a guard in 4D that impedes your progress until you explore the rest of the floor.
Upon reporting the results, you will be rewarded 500en and 1500 EXP to your current party.
Afterwards, you will gain access to the rest of B1F as well as Inver Port and upon returning to the guard in 4D, you will receive three Hammers for forging, namely the Attack Hammer, the Guard Hammer and the Flash Hammer.
Proof of WillEdit
The Senatus wishes to gauge the strength of those plumbing the Labyrinth's depths. If you would answer their call, then defeat Narmer on B4F!
After arriving on B4F, proceed until you are met by the blonde man from B2F that gave you an overview of F.O.Es, which will not be very far. You can now go back to Via Senatus to accept your second mission, which is to defeat Narmer. If you do not initiate the short dialogue with Kujura, you will be unable to accept the mission. The mission is pretty straightforward: explore B4F and kill Narmer.
Afterwards, you can go back to the Via Senatus to obtain your reward (15000 EXP) and continue onwards to the 2nd Stratum; the Undersea Grotto.
Danger in the Undersea GrottoEdit
A woman calling herself Olympia has been seen frequently in the Undersea Grotto. Take her into custody and bring her to the Senatus!
After arriving in B6F and proceeding for a fair bit of time, you will meet up with Olympia, the lady who taught you how to use tents. This time, she tells you about a secret passageway further east and pretty much orders you to go over there. You should proceed until you hit a small room in A5/B5. Once you enter, you will be assailed by three F.O.Es! Fortunately, they do not automatically engage you, and they do not chase you either. You can escape the room fairly easily, as long as you avoid them (they are patrolling F.O.Es). Once you return, she will be angry that you are not dead and will create a convenient secret passage for you.
You are then supposed to go back to the Via Senatus to report this, and receive the next mission. Head back down to where she was and go through the hidden passageway there to B7F. Kujura will talk to you before heading to the nearby campsite, so keep that in mind. Going through the passages, you will be greeted by demoralized sentries and demoralizing Scaled Dragons. You don't necessarily have to defeat the Scaled Dragons, but then you will have to go on a rather extensive roundabout route to get to B8F, where Olympia is. On arrival, she will be mad still and will call an Abyssal Death to defeat you. Hopefully you beat it, and she will still be mad, but a voice will stop her before she does anything bad to you. She will hand over the Sea Bead, and leave. You have to report back to Kujura before you can finish the mission for your reward.
Door to the Deep CityEdit
Use the Sea Bead to locate the enigmatic Oceanmaster Ketos. Meet and speak with this being to learn more about the Deep City, and, if need be, defeat it!
How nice. You now have to go back to the Second Stratum and put that Sea Bead you were gifted to good use. Namely, its main ability is to put an end to those pesky currents. Most of them weren't bad, but the main one that it clears is the one on B7F in 1D. You have to go back to B6F though to find the plinth for the Sea Bead (entrance is in 4B). Once down the stairs, you'll be in the "right" section of B8F. Just head down the rather straightforward path to the end, taking care of the occasional Abyssal Death that patrols the narrow corridors.
And of course, you have to beat Oceanmaster Ketos to get ahead. Surprise! Well, after you've beaten big ol' Moby Dick, the stairs to the Deep City is just past the opposite door.
Congratulations! You've found the Deep City, and unlocked Subclassing (the latter much appreciated by those without a Monk in their original party, no doubt).
Also, if you are aiming for the "Good Ending", answer yes to Olympia's question and Flowdia's question. A bit hypocritical, but still, if you want the "Good Ending", answer yes to both questions.
The Deep City's raison d'etre is the war against the otherworldly Deep Ones. Enter the Hall of Convictions to learn about the threat these monsters pose.
Well, even if you don't feel like subclassing, you do get a few free skill points anyways. Digression aside, you have your new orders, this time from the Abyssal King. Hasten down to the Third Stratum, the Molten Caves. You have to head down past B9F to B10F. Of course, the FOEs of this Stratum are probably a bit scary as of now, so head on past them. It's recommended that you go through this area at night (7pm), as the FOEs as of now only move during the day. Otherwise sneak past them.
Now, once on B10F, you'll wonder where the bloody Hall of Conviction is, provided you've walked into Olympia already, and she's not much of a help. If you did already know, good job. But if you didn't, look across the sea of damage-inducing tiles. You're aiming for the rooms there. However, there is only a door on one side, and it's in 4C, so save yourself some pain and start from the west/left or north/up side. Olympia will unlock the Moon Door that you can't unlock (as of yet).
Get ready for a sort of mini-boss fight as the little child thing spawns two lovely beings at you: a Deep One and a Deep Lady. They won't show up in your Monstrous Codex. After you beat them, you'll be given three options. Think about this carefully. If you want to fight the two Deep Ones again, then by all means choose to charge the little child thing. If not, seek a more peaceful resolution. Once done, you are free to head back to report your success to the Abyssal King.
Keep the Hall of Convictions in your mind if you want the "Good Ending".
Anyways, after this mission, you'll have to choose which faction you'll assist for now. Choosing to do Armoroad's missions will net you the lovely General's Baton, unlocking the Shogun class, while siding with the Deep City will score you the Yggdroid Plan, allowing you to register Yggdroids.
Deep City MissionsEdit
For those of you that chose to go along with the Abyssal King's plan for now, remember that it doesn't matter which side you choose for the "Good Ending". Just as long as you don't choose to accept the "Hunt for the Porcelain Lady" mission at the end of the Fourth Stratum.
Protect the GatekeeperEdit
The Gatekeeper guarding the portal between the Deep City and the lower reaches is a dangerous post. Ensure the Gatekeeper's safety.
After meeting Kujura again on B11F, you will be forced to choose a side. Choosing to side with the Abyssal King, you will be charged with the task of protecting the Gatekeeper. If you ever talk to the Deep City innkeeper, she'll comment on how powerful the Gatekeeper's arms look. Moving along, rush back B11F to B12F, where there are tons of these platforms that will start to slide across the magma once you step on them, bringing you to completely new places (kind of).
Outside the boss chamber, you'll meet up with Kujura again, this time he'll be pretty much a jerk to you. Of course, he voices his intent to slay the Gatekeeper and enters the boss chamber. You'll be urged to take care of him before he does anything bad, but you really have all the time in the world.
Once you enter, lo and behold, he's not there. And obviously, you'll be attacked by the Gatekeeper . And you'll destroy it. And Kujura will laugh at you. If he doesn't, then he's doing it in his head. Well, that went really well. Time to report your failure to the Abyssal King. Oh, he doesn't really care. With a "well, shoot" and the blueprints for his mechanical servants and you'll be back to doing his dirty work again, namely venturing into the Deep One's citadel, the Abyssal Shrine.
Decipher the Shrine's mysteriesEdit
A facility used by the Abyssal King to communicate with Yggdrasil is somewhere in the Abyssal Shrine. Find that place and hear the voice of Yggdrasil.
Off on another mission, you're going straight into the Deep One's spawning pit. Of course, you should be aware of the rather Lovecraftian influence the ENTIRE series has (especially all of the "true" final bosses that are writhing masses of trauma-inducing tentacles). You'll get the rather obscure Powder of Ibn Ghazi to throw on some special wall on B15F. You'll even be prompted to throw dust once you enter the room.
There will be some Q&A time with Yggdrasil before you have to pack up and go report to the Abyssal King again.
Locate the teleporterEdit
There is a teleportation device in the Fourth Stratum that leads to the Porcelain Forest. I want you to find it so we can protect the city of Armoroad.
You finally get to go to the end of the bloody Fourth Stratum without interruption (well, except an albeit minor one). Heading past all of the pitfalls on B15F, you can finally get to the actual B16F that leads to the teleporter.
After duking it out with a number of the endless citizens of the Abyssal Shrine, you get to the final room, which is oddly empty and devoid of random encounters. Well, here comes the minor interruption. Kujura breaks into the room, this time rather keen on disposing you himself. Luckily (or unluckily), Olympia interjects and keeps him occupied. Well, the end of a Stratum isn't complete without some frustrating boss trying to kill you deader than dead, so meet Shin, Kujura's little bottle fairy friend.
After beating her, Kujura will run away and Olympia suggests either getting your reward or jumping straight into the Fifth Stratum, the Porcelain Forest. Of course, you can do both and go directly to the Submagnetic Pole. In addition, Olympia will hand the Moon Key to you, with which you can enter the Hall of Convictions for the "Good Ending", or you go straight for the last mission, to hunt the Princess.