It should have been obvious all along that Nightmare Kartherax is the source. I guess I let my hatred of Shoggoth cloud my judgement. I should have known he's been a hollowed-out husk for years. His mind belongs to the darkness completely.
Defeat Nightmare Kartherax to end the Nightmare for good!
You did it! You've slain the beast! The control it was exerting over the Pirate Soldiers seems to have lifted. I guess time will tell if a Nightmare can stay dead.
Oh? And you retrieved a sample from it? This should be useful...for someone who knows anything about Biology. Maybe Xraal can help with that?