Just to throw in another thought, the dead fisherman on the beach mentions survivors from the crash. A beautiful woman that people couldn't look away from, and an elf.
Who were they? Is it possible they were Z'rell and Ketheric? I guess I'm wondering what was really going on in the attack. Why did the githyanki follow the ship into avernus? Was it for the artifact? Was it because there were chosen of the absolute on the Nautiloid at the same time as the player characters?
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One of the things that don't work for me about karlach's story: why is she so important? Why is she so good at fighting on the front lines? It sounds far fetched and ridiculous. She's level one. I get that she says she was fighting with fire in her blood or some such, as provided by Zariel, but if that's the case, it sounds like the fire in the blood is the valuable resource, not Karlach. Just replace Karlach with some other level one unfortunate and jack the up with the devil juice.
Going in order of your questions;
My theory was that the beautiful woman was a mental illusionc created by the mindflayer in order to lure people to it.
The Githyanki followed the nautiloid into Avernus because killing Illithids is what they do. From my understanding, killing them is priority one over everything else, so following the ship wherever it might go for that purpose makes perfect sense to me. Though it's also implied the artefact is partof the reason as well.
As for Karlach, I assume that Zariel wants her back for a couple reasons. One is that she's been fighting for a while and beyond just fighting ability, she has experience with how devilish stragey works, how to fight demons, experience that takes time to accumulate, so she's got value there. The second reason I expect is spite. I cannot imagine an archdevil would just let her chosen warrior escape. I'd be willing to bet that Zariel's intent is to execute Karlach for her escape rather than just re-binding her.
