It's unfortunate that Larian didn't "clean up" their narrative to a space-and-time-consistent sequence of events.
My attempt to make some sense of it goes as follows.
The key lies in the layout of the Netherbrain's plans. You only get to hear that in the final episode of act 3, but it kinda ties some ends together.
1. The emperor was sent to find the prism. Nowhere is it said that he undertook this mission on the nautiloid that you escaped from. When he found the prism (soewhere in Gith'yanki possession probably), the NB "allowed him to slip the leash". (NB tells you literally) This freed the emperor's mind so he could enter the prism.
2. The Shar commando's were not manipulated by the NB directly, though it probably knew about them and could foresee that they would obtain it. I think it would be unlikely for just Shadowheart to survive the mission and flee from furious Gith'yanki alone. But the NB could have kept an eye on the patrol and a nautiloid "close by" to snatch her up in the possession of the prism, before the Gith caught her. The Gith then start the chase after that Nautiloid.
3. That nautiloid was on a "brain foraging" mission. You can actually ask what they were doing when you speak to one of the dead mindflayers. He tells you they needed to get followers for the absolute. He doesn't mention anything about searching for an artefact.
4. If the NB had the foresight it claimed to have, it could have selected the other partymembers according to the likelyhood that they would succeed in wresting a netherstone from one of the 3 chosen. So this nautiloid would "portal" from one city to another and grab the "chosen" ones, together with a few hundred unimportant "brain vessels" as per their instructions. Astarion states very clearly that he was snatched from the street in Baldur's gate.
5. Another contradiction that may be somewhat explained only by direct intervention of NB, in my opinion, is that they actually manage to tadpole Shadowheart while she has the prism on her. In Last Light Inn, when Jaheira approachhes a tadpole specimen to the prism, it burns up. So NB must have protcected Shart's tadpole against that aura.
