While wandering the Western Sea, Luna can come across Sofia and some of her men on a boat, under attack by Nessie. Should she choose to save them, Sofia invites her to Manil Island afterwards. She attempts to win Luna over, especially when it becomes evident that Luna isn't intimidated by her in the slightest. When Luna tells her the only way to win her over is by stopping the witch hunts, Sofia reveals that opposing the witch hunts was exactly why she was exiled to the island. Telling Luna that not everyone hates the deities, she lends Blue to Luna so that it can help her and keep them in contact.
She isn't mentioned again until the final battle. When Jude attacks Vavelia Village, Sofia fires a long-range artillery to hit Jude and distract him for a second. However, being on a remote island with few supplies, they only had the supplies for a single shot, much to her frustration. After Jude is defeated, Sofia personally awards Luna as savior of Vavelia and will appear at her old house in post-game.
Although Sofia does not personally appear in the main game of Witch Spring 3, she is mentioned in the optional "Judith" side event. Judith tells Johannes that the Dark Company is smuggling supplies to Manil Island so that Sofia won't starve, and Johannes mentions that he'd heard about the princess of Vavelia being exiled there for speaking out against the Pope.
From promotional material for the post-game update, it seems that Sofia will appear at some point in the post-game.