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Warts represent paranoia and the potential return of Sophie the witch. They put fear in Agatha, Hester, and Anadil as they know what Sophiarae is capable of in her evil state. Just seeing a single wart causes Agatha to distrust Sophie and sends her to Tedros in a desperate attempt to stop Sophie from becoming a witch. Although it is revealed that the warts did not exist, none of the main characters are able to fully trust Sophie. They constantly wonder when she will return to evil. Ironically, it was not the warts that lead to Sophie turning to evil. It was Agatha herself, who believes that Sophie could never be more than a witch.