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When I entered the southern dwarven kingdom, beat the war machine and watched the event with the northern dwarf lord, after I tried to exit the inn, the scene where the northern dwarves attack suddenly started, meaning I had to do the northern battles with just Dominus and Mercury (fun.) Afterwards, the scene with the northern dwarf lord repeated with Dominus invisible. After resting at the inn and saving, the game seemingly went on as normal.

Yes, both before and after getting the book. Second time got me a Tear Of The Sun. Funny thing is, after saving and loading my game, I tried to enter the cave again, but it still said that the cave is flooded. After that, I tried to pay the mayor again, and he gave the hint again, after which I could enter with no problem.

OK, I got the item. Trouble is, despite the game saying Mercury learned the spell, when I try to enter the cave it just says the cave is flooded. The Aqua Lung Spell is in my key items, but not in Mercury's spell list. Is this another glitch, or do I have something else I need to do?

Near the village where you get the boat, there is a flooded cave that I can't figure out how to enter. Any hints?

Got it. What tripped me up was that the three labyrinths had different amounts of orbs. That said, there's something I feel I should inform you of; after I got the three labyrinths completed and rescued Oriel, when I returned to the library and freed the elemental beasts, then entered the underground door (no need for any new keycards, the door just opened.) 

After entering, the scene with Kamran and Mercury repeated itself. After the scene ended, I beat the high priest and entered the knife chamber (didn't grab the knife, just took the two treasure chests and left), after I tried to leave, the cutscene where Melody shouts at Kamran to tell him the fort is under attack also repeats, and from there I went to the fort, and Dominus was back in the cell. 

After talking to him, I was automatically sent to Red Wall Village, and Mercury left my party (probably because he leaves when the scene is originally shown.) Anyway, I reloaded my save from the knife chamber, and after the Melody scene forcibly removed me from the library I just proceeded to the next area, where the game continued on as normal.

Help! I'm currently in the tower with the three mazes containing elemental orbs. I found all three, but I don't know where to go next.