I haven't done the evil ending, but it did look like a really bad idea. After learning how those three who'd prepared for years had failed to control the elder brain, what sort of person is going to go "do you know, I reckon I could control it"?
So, yeah, the nether brain probably just regains control when the Emperor runs out of energy or something, and tries to implement the Grand Design.
Eh, that's just how I saw it. Orin, Gortash and Ketheric already struggled to keep the Netherbrain under control pre-powerup, I didn't really get the impression Tav, become illithid or not, has it permanently in the bag. Hence the 3 months before it all just falls apart, starting from the most tangible threat: the army. Someone's going to come and murder their way up the chain of command, just like we did it.
Well the game relentlessly implies that the Three's downfall was firstly their constant backstabbing and mismatched coordination, which you are not afflicted by as the Netherbrain's sole master, and secondly their lack of foresight into the Elder Brain's behavior as humanoids, another aspect which is presumably remedied by your transformation, so at least if we take the game's narrative at face value, then your reign over the Netherbrain should last considerably longer, if not permanently.
The biggest risk I perceive in that regard is actually not simply you randomly and sponatenously losing your grip over the Netherbrain for unspecified entropic reasons, but rather an alliance of several Elder Brains succeeding in exerting enough psionic power to disrupt your control in a bid to restore the Netherbrain's autonomy as opposed to striking deals with you.
