Here's my basic understanding of the plot, I could be way off but this is how I understood it.
-The nautiloid was sent by The Absolute to kidnap people and put the latent tadpoles in them. Dark Urge is put there intentionally by Orin, Tav was kidnapped from Baldur's Gate.
-The tadpoles were modified so that they would stay latent in the host's body and not begin ceremorphosis immediately so that The Absolute (the Netherbrain I think?) could spread their influence and turn as many people as possible all at once. In act 2, if Gale blows himself up in the room with all the bad guys, the tadpoles all trigger at once and Baldur's Gate is overwhelmed by a horde of illithids.
-This is me speculating, but I suspect that the Emperor put himself into the prism because as an illithid who wasn't attached to the hive mind if he came into the elder brain's psychic influence he would have been dominated instantly and returned to the hive mind.
- This is the one I'm the least clear on, but I think he wants to either dominate the netherbrain himself and sees the main character as his best chance to, OR it's simply a matter of self preservation to avoid being returned to the hive mind or slaughtered by Orpheus.
