The Emperor led the expedition to get the prism from Vlaakith. Meanwhile, Shadowheart's team was stealing the prism.

The Emperor captured Shadowheart after the prism had already been stolen. Being near the prism gave the Emperor back his identity.

At this point, the Emperor had the prism and was *supposed* to have returned the prism to the chosen of the dead three. However, he quickly devised a plan to fight against the cult of the Absolute.

That plan included getting victims to tadpole. That's why the nautiloid is suddenly attacking cities in such a brazen unheard of manner. He's gathering people to be tadpoled so that he can use them to fight against the Absolute.

The Emperor manages to tadpole some of the captured people, as we see in the opening scene. We also see a dead mind flayer in that scene, which suggests that the Emperor has gone rogue and had to kill some of his crew to enact his plan.

He continues trying to get more victims.

Unfortunately for the Emperor, the githyanki respond to the theft of the prism by sending dragon riders. They've now caught up to the nautiloid. The Emperor pilots the ship to the nine hells to escape the attack.

Some of the prisoners break free. It is around this time that the Emperor enters the prism.

The escaped Tav and Lae'zel make their way to the helm.

Note: Us tells Tav that Shadowheart will be safe if she is left in the pod. That's because Us is taking mental cues from the Emperor, which is ultimately what "tainted" Us away from the Absolute.

Before the ship crashes, Tav is struck in the head by a piece of the ship. This is an unlikely event that is probably caused by the Emperor. It leads to Tav falling out of the ship and ultimately being saved by, of course, the Emperor. All so that Tav and company can become the weapons of the Emperor who knows he needs help to defeat the Absolute. Hence the aforementioned desperation.

*

Just look at the armor in the opening sequence and compare it to the Emperor's armor. It's obvious. That coupled with the passage from the book in the vault make it pretty clear what's happening in the plot.

This is the rough sketch of what's going on. I have no doubt that Tav was tadpoled by the Emperor. Somewhat clever of the writers if you ask me.