I keep wondering, how did the companions end up on board the Nautiloid? No one says, and we don't get an option to ask.
1. Shadowheart. Did she sneak on board and steal the weapon? Or did she get her hands on the weapon somewhere else, and then ultimately get captured and taken aboard the Nautiloid?
--at least two groups knew the weapon was on the Nautiloid. The githyanki and the True Souls. Did they also know it had been stolen by a Sharran agent who had been captured by the Mind Flayers?
___
2. Astarion. He says, "They took you, just the same as me." He said he was in Baldur's Gate when those beasts snatched him.
--was he taken randomly? Or is it more likely that his capture was arranged? And if so, by whom? Cazador, perhaps. Did Cazador arrange for Astarion to be captured by the mind flayers in some sort of trade or bargain?
___
3. Wyll.
--were they after Wyll or was he just in their way of getting Mizora?
___
4. Gale.
--there's Netherese magic inside of him, requiring him to feed off of magic items.
--there's Netherese magic doing something to the tadpoles.
--coincidence?
____
5. Lae'zel. Her creche is in the Tears following the moon. How the heck did she end up on the Nautiloid? It's not like she has some story about being in a patrol that was overwhelmed by mind flayers.
--so she just happens to be on the same Nautiloid that another githyanki creche is chasing because they know the weapon is on board?
--did Lae'zel's creche know the weapon was on board? (Lae'zel sure doesn't seem to know anything about the weapon.) Did her creche know she had been captured?
--it all feels too convenient; Lae'zel just happens to be a prisoner on board while another creche is chasing the Nautiloid for reasons not having to do with Lae'zel.
--no, Lae'zel almost certainly has to have something to do with the weapon, just somehow unknowingly.
--or maybe there's betrayal among the creches? It's portrayed as a gith artifact. Was it stolen, or did Lae'zel's creche allow it to be taken by the Sharrans? After all, the artifact seems to go to who it wants, as if it's sentient.
____
6. Karlach.
--does her story add up? She's on the front lines of the war, sees the Nautiloid, flies up to it somehow, gets on board in an effort to escape the hells, and then...
--gets a tadpole in her eye?
--there wasn't much time for her to get captured and have a tadpole forced into her eye. The ship was under attack and seriously damaged by this point, and it's questionable how many mind flayers were going about their business.
--these are tadpoles that have to be put into someone's eye. It's not like catching the cooties because she got on board.
***
There's something else I also think is worth considering.
The opening scene shows a mind flayer put the tadpoles in Tav and Lae'zel's eyes. This is before the gith attack. This is before the Nautiloid went to the hells and found itself attacked by devil kin.
There were dead mind flayers laying all around. Why? Who killed them? What happened right before that left mind flayers dead?
Almost as if there was a rebellion on the ship.
Did one faction of the mind flayers change the plans? Is it possible that the regular mind flayers were delivering the bodies to Moonrise, but then another mind flayer betrayed the cause?
Perhaps that led to a modified tadpole getting put into the origin eyes?
To your point, I think we can assume that the nautiloid has been in operation for some time, it might even have been to Avernus already. I initially thought that part of why our indoctrination went wrong is because the Mind-Flayer was rushing our process in order to refill the ranks up. We see that they have a tank that accelerates the process greatly.
The main point though is this, the Artifact is Gith in origin, it's probable that the Mind-Flayer's stole it from them, suffered serious damage and casualties doing so, forcing them to raid for more thralls and hosts, even while being pursued by Gith, furthermore this raid by the Mind-Flayers on the Gith could be where they got Lae'zel, if she wasn't part of the party we see attacking the nautiloid.
With this in mind, we can't really take for granted how long we've been 'On Ice' in the nautiloid after being nabbed, the opening movie is of Elturel, most of our characters are from Baldur's Gate, Lae'zel is from Creche K'liir, Karlach hopped on during a jaunt in Avernus, Shadowheart's cult operates in Baldur's Gate too...but she's the one who has the Artifact, she also shows great animosity to the Gith, so I'd go so far as to say the Sharran commandos didn't assault the nautiloid but a Gith outpost where the Artifact was kept, only to be nabbed by the Mind-Flayers...coincidentally? or to in turn gain the Artifact
