There's some big Act 3 reveals that indicate what happened. I'm still trying to make sense of them because I think the rewrite made a mess of it.
Gortash found out about the Astral Prism and, as he was worried about it's anti-psionic capabilities, sent The Emperor along with a tadpoled strike team and a nautiloid to steal it. The mission is successful, apparently, and the Gith give chase. Somehow Shadowheart ends up with the Prism despite not being part of the mission and being locked in an illithid tank. A Mind Flayer who looks like The Emperor tadpoles the protagonists, who escape and take control of the ship. I even think it's The Emperor who is the Mind Flayer who looks at the protagonist just before they get flung out of the nautiloid. At some point, The Emperor gets aboard the Astral Prism, and saves the protagonist from falling to their death. The Emperor may have been only pretending to work for the Absolute throughout this process.
Last edited by Milkfred; 13/08/23 05:34 AM.