Honestly, I’m fine with the Emperor’s storyline. It makes sense to me, until the final scenes with him. The thing I would change is:
When your character says that they won’t give the Emperor the netherstones or let him assimilate Orpheus, as many have mentioned, he gets spiteful and rushes off saying he’s joining the brain. Then in the final battle he comes across as PROTECTING the brain. But what if instead of flying off to the brain when refused the netherstones, the Emperor says “This isn’t over” and leaves. The implication being that he felt outmatched in that moment and was leaving for reinforcements (i.e., a dominated dragon!). Once he knew that you couldn’t manipulate the brain, he no longer had use for you and abandoned you to make different arrangements.
And when he arrives atop the netherbrain, THEN the implication is that he is there to take the netherstones and assimilate Orpheus by force this time. The further implication is that the Emperor is not okay with anyone else dominating the brain (Orpheus as mindflayer), so he wants to dominate the brain for himself. Not only for ultimate freedom over it, but to gain back all of the power and influence (and far more) that he gained dominating Duke Stelmane. He has a taste for power. Now he’s here to thwart the main character and make the Sword Coast submit to HIM. THERE. The ultimate villain of the game, who has been with you since the beginning and you never even knew.
It could be clearly explained by dialogue and work well. Maybe explaining that he even tadpoled you to use you to get back to the brain. He certainly would work better as the ultimate villain than the netherbrain itself, which is invisible and intangible for 98% of Act 3.
Overall I’m extremely happy with how the game ended now that they’ve added an epilogue! But I think they could tweak the ending to make it work a lot better, and tweak it pretty easily.
