Why do you think she disappears after the first section of the book?
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The Comtesse is a French aristocrat rescued by the Scarlet Pimpernel in the opening section of the novel, but her husband is left behind, prompting the dramatic rescue that dominates the novel's main plot. She does not like Marguerite St. Just because she thinks that she caused the demise of the St. Cyr family by denouncing them to the tribunal. I don't think the author has much use for her character after the first section of the novel.