What was happening at the start of the game?
No, really.
When you start the game, it appears pretty simple: a nautiloid has arrived at Baldur's Gate and come under attack from the Gith. It appears that Lae'zel and the various origin characters are already on the Nautiloid at this point. A Mind Flayer -- and more on this guy in a bit -- sticks the tadpole in your eye, you escape, and it's off to the races. You encounter Shadowheart, who bears an odd artifact, and then manage to bring the nautiloid back to Faerun after a brief detour through Avernus where Lae'zel collects a flaming sword souvenir. All pretty simple, right?
Things get complicated by certain revelations in the last act of the game. I'll spoiler these because they're pretty big, but they concern things you can find in a certain vault in the Baldur's Gate.
The nautiloid was out to steal the Astral Prism from the Githyanki. Okay, makes sense. Gortash used The Emperor to do it via the Absolute elder brain, along with a strike team of tadpoled individuals. Okay, fine. But this means that it is The Emperor who tadpoled you in the opening cutscene (and if you don't believe me, go back and check -- it matches his outfit and unique look exactly.) So, why? And if so, why do we not get the chance to call him out on it? Was The Emperor already getting out from under Gortash's thumb? If it was Gortash's mission to grab the Astral Prism, how did Shadowheart end up with it sealed in her pod? How many stops did the nautiloid take if it picked up Lae'zel, Gale, and everyone while apparently being on a top-secret mission? When and how did The Emperor get inside the Prism? The Emperor says he entered it the moment he found it as it freed him from the Absolute the moment he saw it, but that still raises questions -- did he find it, enter it, and Shadowheart found it, only to get sealed in a changing pod? If he entered it the moment he found it, then is it a coincidence that the Mind Flayer in the opening cutscene is wearing his unique outfit? Who was this strike team, and did they all perish? How does The Emperor need to keep Orpheus' asleep tie into things, if the Astral Prism was just chilling somewhere?
There may be elements that I've missed (for example, I've heard that Shadowheart says that the Sharrans were attempting to undermine the mission) but I'm not sure if all the pieces fit together.
