I feel like a lot of these takes aren't based on what we learn from Gortash's books in Act 3.


Gortash and co. find out about the Astral Prism, referring to it as the only thing that can disrupt their control of the Elder Brain, and that it is in Vlaakith's possession.
They send the Emperor and a team of tadpoled thralls aboard a nautiloid to steal the artifact from the Gith.
Viconia catches wind of this and sends Shadowheart and co. to get the artifact first.
Gortash's team steals the artifact, and the Absolute releases control of the Emperor (for some reason.) Leading the Emperor to believe the Prism freed him.
The Gith pursue the nautiloid, which reaches Baldur's Gate, and the fight continues through the planes, including Avernus.
A bunch of people are abducted throughout this time, including from as far as Waterdeep.
The Emperor ends up in the Prism (after potentially tadpoling the player) without anyone noticing.
Tav and co. escape, nautiloid crashes, etc.

Honestly, if they changed Daisy, the Emperor, Absolute, etc. then I think the beginning is likely less coherent now.