I think that the assault on the ship by the Gith has already been ongoing for a while by the time the game starts, and they are responsible for the dead mindlayers.
I don't get that impression.
The scene starts. Mind flayer comes through the door. There's no sense of urgency or concern. It takes the time to infect Lae'zel, and then Tav.
The mind flayer leaves, glancing at a dead mind flayer on the way out. It goes to the helm and begins the attack on the city (Elturel, I believe).
Now the gith arrive, and now there is a sense of urgency. The attack is on. The mind flayer responds. The dragons engage in battle with the ship, and the mind flayer takes evasive action, traveling dimensions.
This scene is not the picture of an ongoing attack from before the scene started. It's the picture of:
Something big happened and upset the natural balance on the ship. Now, because whatever went down just happened, this mind flayer is conducting business, infecting the origin characters. In fact, the mind flayer is bent on acquiring even more people. This is an epic raid on a city, almost as if the mind flayer were desperate for additional people.
The gith arriving complicate matters.
I don't remember if Shadowheart and company raided the Gith or the Mindlayers to get the Dodecahedron. If it was the Mindflayers they might also be the ones responsible for the dead crew.
I don't think there's anything to remember because I don't think it was ever said one way or the other. Please correct me if I'm wrong.
Yes, Shadowheart and friends might have been responsible for the mayhem on the ship prior to the start. That was my initial thought, but I don't see any of Shadowheart's people lying around dead.
