Duncan and Isadora Quagmire are introduced in The Austere Academy when they invite the Baudelaire children to share their table in the school cafeteria after an unpleasing encounter with their soon to be arch rival Carmelita Spats. They are named after Isadora Duncan, a famous dancer whom died after being strangled by her own scarf. Their skills/interests are quickly established: Isadora recreationally writes poetry, specializing in couplets; Duncan is an aspiring journalist who makes notes about his surroundings. Each triplet carries a notebook wherever they go. They explain that their parents and brother Quigley perished in a large fire and prefer to be referred to as triplets; parallel to the Baudelaires and the Baudelaire fortune, they stand to inherit the Quagmire Sapphires when they come of age. Duncan and Isadora share classes with Violet and Klaus respectively and a close friendship develops between the triplets and the Baudelaires. When Count Olaf appears as Coach Genghis, the Quagmires decide to involve themselves; they research Olaf's past crimes in old newspapers in the school library and sneak out of Vice Principal Nero's concerts to spy on him and the Baudelaires. The Quagmires' last attempt to aid the Baudelaires (ill-advised, according to Lemony Snicket) involves the triplets disguising themselves as the Baudelaires and ends with Olaf abducting them when he flees Prufrock Preparatory School with the help of the white-faced women, intending to obtain the Quagmire Sapphires. Before they are taken away, Duncan shouts the phrase "VFD" to Klaus, saying that it is something awful that he and Isadora discovered while researching Olaf's history.
In The Ersatz Elevator, the triplets are discovered locked in a cage at the bottom of an unused and apparently pointless elevator shaft at 667 Dark Avenue, the address of the Baudelaire children's latest guardians Jerome and Esmé Squalor. They are described as having a 'haunted look' about them. They know little about Olaf's current scheme, but they are able to reveal that he plans to smuggle them out of town. The Baudelaires return to their home in the penthouse to prepare blowtorches to free the triplets from their cage, but find them gone when they return to the bottom of the shaft; the removal of their cage exposes the shaft's true purpose as a secret tunnel. At the end of the book, Olaf, Esmé and the Hook-Handed Man successfully escape with the Quagmires, who had been hidden inside a red herring.
Duncan and Isadora make their last appearance in The Vile Village (though they are referenced regularly for the rest of the series). The village caretaker Hector, with whom the Baudelaires live, upon hearing about the Quagmires, gives to them a scrap of paper upon which is written a couplet which they recognize as Isadora's poetic style. Hector says that he found the paper at the bottom of the Nevermore Tree, where the crows that populate the village roost every night. More couplets are found at the bottom of the tree as the story unfolds and the Baudelaires soon discover the couplets, when put together, reveal where the Triplets have been imprisoned within the village. The Baudelaires eventually free them and they are pursued along with the Baudelaires by the villagers to the outskirts of town. Once there, Hector appears in his self-sustaining hot-air balloon mobile home. The Quagmire triplets climb onto the home safely but the Baudelaires are thwarted in their attempt to do the same by Esmé Squalor, disguised as Officer Luciana, using a harpoon gun. The triplets throw their notebooks to the Baudelaires and beg them to read them to discover the secret of VFD, but Esmé also destroys the notebooks using the gun. Duncan and Isadora fly away in the home with Hector, safe from Olaf's clutches. Their now fragmented notes prove to be of some assistance to the Baudelaires in learning more about V.F.D, Olaf and their own connections to the organization.
Isadora and Duncan were attacked by V.F.D. eagles, which took out the balloons supporting them, just as they meet up with Quigley. As a result, they were sent down, taking out the Queequeg directly below them. They are taken by The Great Unknown.