Yeah, that's a bit of a thing that doesn't make sense in the plot as it currently is.
If you play the Dark Urge, it is revealed that
Orin had placed you there, and you were the only origin that wasn't kidnapped at random. So, the Nautiloid was in fact, under the control of the then subjugated Absolute
The Emperor makes zero sense, at all. Don't even get me started, or it'll be the third thread where I start ranting. But.
His being in the Prism is a very recent thing. Ehm, let's TRY and do this chronologically.
Orpheus and Vlaakith are enemies, Orpheus fought Vlaakith's dudes and was imprisoned in the Prism.
Prism was in the care of Vlaakith's men, but Emperor stole it.
Then, someone on either side of the Gith war must have taken it, because Shadowheart under orders of the Sharran Sect, stole it from the Githyanki.
From there on, I think the Emperor just went with 'the adventurers that have the Prism', because otherwise it would fall in either the Absolute's hands, or the Gith's, and he hates both. Sometimes.
