I can forgive time inconsistencies but motivations have to be clear.
So... did I get it right: the whole plot was the master plan of the Netherbrain?
- Dead Three, frustrated with lack of power, decided to switch from pure godhood to netheresian magic using the Elder brain.
- Elder Brain calculated the outcome and pretended to be enslaved, allowing DT to create an army of mind flayers - his future thralls.
- While they are on it, ED shares information about the Astral Prism and the only being that can potentially destroy EB. So, DT began the search.
- Unhappy with DT actions, other gods became curious about the Prism as well, plus, Githyanki want it back.
Up to this point, the plot works for me. The rest demands heavy headcanoning.
- The Emperor finds the prism and enters. Why?
I can live with the idea, that Orpheus could be killed only inside the prism and EB had to motivate the Emperor to enter (even supplying some intellect devourers for help), but the rest becomes problematic. There are two options:
1. EB keeps control over the Emperor the whole time. Killing Orpheus proves to be difficult, so, the Emperor needs outside help and recruits the gang.
+ Explains the schizophrenic behaviour of the Emperor if you insist on freeing Orpheus (his return to EB and desire to destroy Githyanki).
- Does not explain why the Emperor wanted to kill EB (and he does if we side with him).
2. The Emperor is honestly free the moment he enters the prism, remembers himself and sets his own plan to kill EB. Something EB could not foresee.
+ Explains everything but the Emperor's return to EB.
Maybe the latter can be explained by the strike of a deep depression of the human part of the Emperor: everything is lost, no point in struggling, he might as well return to EB and forget himself again. Sort of a suicide.
Durge wins over Tav for the netherstones (it makes sense to keep the owner alive to keep the stone active). But Tav wins in reactivity (or, better say, does not suffer that much from the absence of it).
The option of mediating relationships between Orpheus and the Emperor is severely lacking, though, in any case. Hope, it will be added.