Spoilers for A Series Of Unfortunate Events Season 3 ahead! Duncan and Isadora Quagmire are two triplets, not twins; they lost their brother Quigley in the fire that destroyed their home. When A Series Of Unfortunate Events returns for Season 3, Duncan's fate is revealed to be not exactly what most of the characters initially believed. Similar to Lemony Snicket's books, Quigley survived the Quagmire fire — he's the mysterious person that Madame Lulu heard about.
He's the one waiting for further instructions at VFD headquarters, not one of the Baudelaire parents. Mrs. Quagmire lead Quigley to an underground passageways underneath their library, but is unable to save herself or unite all three children. Duncan and Isadora are sent to Prufrock Preparatory School, and Quigley retraces the steps of his siblings and the Baudelaire orphans — until he finally encounters Violet and Klaus at Mount Fraught.
Quigley is also more entrenched in VFD than the Baudelaires, having been recruited by volunteers. In the books, he spends an extended period squatting in Dr. Montgomery's house and works alongside Jacques Snicket, but in the series its Jacqueline, Kit, and Larry Your Waiter who find him. His life wasn't easy after his parents died, but at least Quigley was not being chased and tormented by villains at every turn. His life was more the kind of adventure kids dream of having.
Quigley's speciality is cartography, the study of maps, but this isn't touched on that much in the Netflix series. All children with VFD parents seem to have a primary subject of interest: Violet is an inventor, Sunny cooks, Klaus researches, Fiona is a mycologist, Isadora is a poet, and Duncan is a journalist.
In both the TV series and the book series, Violet has a brief flirtation and romantic moment or two with Quigley. It's interesting, because Duncan seemed to have a crush on her at school that she reciprocated. There's nothing wrong with it, of course, but there does seem to be a pattern of women in VFD having multiple male suitors. Violet, Duncan, and Quigley are repeating their parents' patterns without realizing it.
At the end of the series, Quigley is reunited with Duncan and Isadora on the Self-Sustaining Hot Air Mobile Home after receiving their distress signal. That's the last we see of them.
This is much more pleasant than the Quagmires' ultimate fate in the book series. In the books, when Kit washes ashore the island where the Baudelaires are hiding, she tells them that the balloon was attacked by eagles just after Quigley reached them, and crashed into the Queequeg submarine. The three Quagmires were stranded in the water with Fiona, Captain Widdershins, Phil, Hector, Kit, and the Incredibly Deadly Viper when the Great Unknown (the potential sea monster shaped like a question mark) approached and pulled everyone but Kit and the snake under the sea. Yikes! Did they all die? That's left unclear, as we naturally don't know what the Great Unknown is.
A Series Of Unfortunate Events is concluding with Season 3, having reached the end of what's written in the books, but dangling threads like this leave the fictional franchise open to a little more. No matter what happens next, they're together again, and in a world this bleak that's what matters most of all.