It must have been Shadowheart that somehow, as a level 1 cleric, managed to nick the prism from Vlaakith. She then somehow incurs an extra bit of memory loss and winds up in the Emperor's nautiloid. How did that happen? Was it a coincidence? It could be that the Emperor somehow knew Shadowheart had the prism on her, so he abducted her. Mission accomplished, right? Why did he go plucking people off the streets in some city somewhere?
Shadowheart, like the others, was above level 1 before the tadpole removed her powers. The blade of frontiers was taking down minotaurs before he struggled to take on a goblin. And the document in the Sharran Cloister tells you that she was healing - the others in the group were more powerful.
Likely timeline
1. SH's team gets artifact
2. Gith slaughter everyone but SH, she grabs artifact and runs
3. Emperor's nautaloid shows up and slaughters and captures Gith
4. Emperor get artifact and goes rogue
5. Emperor attacks some random city and grabs people.
6. Emperor tadpoles Tav and co. The goal is to have an army of illithids and half illithids to take on Netherbrain
Attacking a random city with a nautaloid is not Gortash's plan. He wants everything hidden until the last minute. Attacking a city is part of a desperate attempt on the part of The Emperor to kill the brain before the Gith or the brain can respond.
But it turns out he is stuck with a small handful of adventurers not a the small army he wanted.
