I am very passionate about the lack of logic in the current ending so I'm going to post my thoughts
Emperor should absolutely not side with the Netherbrain in the case of the true souls freeing Orpheus. Siding with the Netherbrain means it loses its freedom, which is exactly what it has been working against the entire story; That is the exact opposite of what it wants.
Its very clear that the Emperor is not afraid of taking a risk: It is taking a risk by consuming Orpheus. It clearly states earlier on that consuming Orpheus is a massive risk because it doesn't know whether by consuming Orpheus that it will obtain his powers to disrupt hive mind communication. Consuming Orpheus brings with it the non-0% chance of the Emperor not gaining Orpheus's hive mind disruption powers. The only reason the Emperor feels it must consume him is because this is its last-ditch attempt to take down the netherbrain.
So, in the light of this, why can't the Emperor accept the risk of Orpheus turning on it and killing it once he is freed? Logically speaking, it has either:
- a 100% chance of being controlled by the netherbrain and either being its puppet again or dying to the true souls
- a greater than 0% chance of Orpheus sparing it and then killing the netherbrain together
Considering the Emperor knows that only an illithid can control the netherbrain, it's highly likely that it realizes that it can find a way to negotiate with Orpheus. After all, Orpheus logically speaking has basically 2 options:
- Kill the emperor and have to turn illithid/have someone else who is not full-illithid become full-illithid
- work with the emperor and take down the netherbrain
and for the argument that, "Orpheus doesn't know if he can trust the Emperor; What if he turns on them at the last moment, controlling the netherbrain rather than destroying it?", I have this response:
Orpheus still retains hive-mind disruption, therefore he (and the true souls) would be unaffected by the Emperor's subjugation of the netherbrain. Because of this, if he for a moment thinks the emperor is going to turn on them, he and the true souls can kill it. Therefore, the Emperor, who is so concerned with its own survival, should definitely be trustworthy. After all, a mind flayer with a common goal as you is the only time where it is okay to trust a mind flayer.
