Fiona's father moved away when she was young, but her mother was remarried to Captain Widdershins. He continually tells Fiona that her mother died in a "manatee accident," though Fiona doesn't believe it was an accident; indeed, towards the end of the book, it is revealed that Widdershins was wrong about this. (Later, in The End, an unrelated character named Miranda Caliban claimed her husband Thursday had been eaten by a manatee to cover up for the fact that they had broken up. It is unknown whether these two incidents are related.) Fiona is the sister of Fernald, the Hook-Handed Man, and although their last names are unknown, it is made clear that they are not part of the Widdershins family. Fiona is fiercely loyal to her brother.
Fiona first appears in The Grim Grotto, when Violet, Klaus and Sunny Baudelaire enter the Queequeg. Though she is not part of the Queequeg's "Crew of Two," she is the ship's head engineer. Fiona is the first non-Baudelaire that can actually understand some of Sunny's utterances. Later, Fiona goes with the Baudelaires into the Gorgonian Grotto to look for the sugar bowl, but when the four children come back, empty-handed, they find the Queequeg deserted; Captain Widdershins and Phil had been convinced by an unnamed woman to abandon the ship. Count Olaf then captures the submarine with his own, the Carmelita, and takes the Baudelaires and Fiona to the brig to be tortured by the Hook-Handed Man, who turns out to be Fiona's long-lost brother Fernald. The Baudelaires and Fiona persuade Fernald to join them and help them escape. The Baudelaires escape, but Fiona and Fernald are caught and tell Esmé Squalor that they support Count Olaf. At this point, Esmé begins to call Fiona "Triangle-Eyes," due to the triangular shape of her glasses. Later, Fernald persuades Fiona to really be part of Count Olaf's troupe. Violet is the first to truly see Fiona's volatility.
Fiona and Fernald do not appear in The Penultimate Peril, but Count Olaf says that the two stole the Carmelita. In The End, it was revealed that both returned to the Fire-Fighting Side of V.F.D., but they were both sucked into The Great Unknown.
Fiona kisses Klaus before she leaves with her brother in The Grim Grotto, suggesting some romantic involvement. Klaus appears to return her feelings; he reacts to her post-kiss vanishment with, "How could someone so wonderful do something so horrible?" In The Penultimate Peril, Snicket mentions that "Fiona broke Klaus's heart," which is repeated multiple times in The End. Kit Snicket tells Klaus before her disappearance that "Fiona was so desperate to reach [him]," and "she wanted [him] to forgive her as well."