At any rate, the Emperor, when faced with a PC that wants to free Orpheus, joins the Elder Brain. Why?! This does not make sense. Was the Emperor evil all along? I don't think so. When siding with the Emperor, he will destroy the Brain, so he was sincere with his intentions, right?
I'm not convinced he's even remotely benevolent.
He wants you to "evolve" into a mind flayer throughout the game after all... and I have no doubt that he's after the Grand Design with himself in control. He's an Illithid after all.
But the why does he destroy the Brain if you side with him?!
Still makes no sense
My best guess is that the brain's continued existence would be a danger to his plans
The whole ending is inconsistent and feels somewhat rushed to me.