Well, he's trying to groom you into becoming a mindflayer for one which means death at best and the destruction of your soul at worst (I'm not sure if the lore is very clear on this but Withers says the soul gets destroyed by Ceremorphosis). He also wants you to be complicit in killing Orpheus and thereby robbing the Gith race of their future. Oh, and he tries to convince you to kill Minsc for no apparent reason.
If you choose to help the mindflayer in the windmill, it reveals to you that it is not infact the former person you're speaking to, but the tadpole that infected them. Going by this, the person 100% dies. I think this is one of the reasons he really didn't want you talking to it. Also, if Orpheus chooses to go through ceremorphosis, then he will tell you how he's struggling to keep his mind intact (I have a suspicion his mind only persisted rather than the tadpole taking over because of his absurd psionic power). This makes The Emperor's plot to groom you into a mindflayer all the more insidious.
I think his choices in the Astral Prism make so much more sense if you view him as purely selfish. He can not exist as an individual as long as the Elder Brain exists. His self preservation is more important than preventing the enactment of the Grand Design. Honestly, it would have been cool to have an option where you can persuade him to give a chance with Orpheus, and then persuade Orpheus not to flat out kill him. After all, there NEEDS to be a mindflayer holding the stones in order to succeed. How absolutely selfless Orpheus is in order to prevent the Grand Design from spreading should be enough evidence that he would allow the mindflayer to aid us.
The real option that seems to be missing is persuading The Emperor to give Orpheus a chance regardless that The Emperor is demonstrably evil.
