Karlach leaving and not joining you right away is lame, imo.
She has a tadpole. Everyone and their grandmother is already after you, and her, because you are all infected. You're all going the same way. Why would she NOT join you?
I really think this is just stand-in filler at the moment. Just like Shadowheart's recruitment changed, I suspect Karlach's will be different in the future.
Your theory about the Sword of Justice is interesting. It's not something I previously considered, but it makes sense. They're using her own sword to hunt her down and kill her.
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There's a pod along the river that smells bad, basically like sulfur if I recall correctly. Does anyone know who was in that pod? Was that Karlach's pod? Mizora, maybe?
And why's there a coffin in the middle of the river by a pair of boots near the owlbear's lair?