The underwater ship was named after a character in Moby Dick by Herman Melville.
The submarine was built by Kit Snicket, Widdershins for the use of became its captain, and he ran the submarine with Mrs. Widdershins. Over the years, the "crew of two" changed under Widdershins, while his stepdaughter, Fiona, lived aboard the submarine. He refused to consider her a part of the crew, and withheld important information about VFD from her.
Captain Widdershins and Fiona managed to rescue documents, including Klaus Baudelaire's decoding notes, from Josephine Anwhistle's library after the house fell into Lake Lachrymose. After that, they were ordered by VFD to travel down the Stricken Stream and find The Sugar Bowl.
Violet, Klaus, and Sunny Baudelaire were rescued by the captain and his crew after being washed down the river from the Mountains. Later, the Great Unknown (shaped like a question mark) and an octopus shaped vessel appeared on the sonar screen. The octopus vessel turned out to be Count Olaf and his troupe's submarine, while the question mark, still unknown, is later referred to as "worse and more treacherous than Count Olaf himself." Directly afterwards, Count Olaf catches up to the Queequeg and shatters the windows, which are later repaired by the Baudelaire and their acquaintances. Sunny chewed some gum that Phil got from Lucky Smells Lumbermill and used it as an alternative to glue.
After the disappearance of Captain Widdershins and Phil, the Queequeg was captured by The Carmelita, an octopus-shaped submarine used by Count Olaf. Subsequently, Fiona joined the crew of The Carmelita in order to stay with her brother Fernald. However, she helped the Baudelaires escape and take the submarine to Briny beach, where they meet Kit Snicket. Kit managed to reunite with the Widdershins family aboard the submarine.
The Queequeg sailed out to sea to find the Self-Sustaining Hot Air Mobile Home, which was carrying the Quagmire triplets and Hector. The balloon was taken out by the fire-starting side's eagle, causing it to crash onto the Queequeg. There, the group (minus Kit) were taken by the Great Unknown.
The boat had a "Crew of Two," originally consisting of Captain Widdershins and his wife. After her death, her position was then occupied, on different occasions, by Jacques Snicket, Lemony Snicket, and a woman who later turned out to be a spy. Kit Snicket helped in the construction of the submarine. At the time of the Baudelaire orphans' arrival, Phil, formerly employed Lucky Smells Lumbermill, was working as the submarine's chef. In the Netflix adaptation, Fernald is shown to have joined the crew with his sister, and in a brief scene in The End, it is hinted that they were reunited with Captain Widdershins.
The Main Hall is the center of all operations aboard the submarine. It's said that there are pipes on the ceiling, pipes on the floor, and pipes sticking out from the walls at a variety of angles, and between these pipes is a bewildering array of panels with knobs, gears, and tiny screens. The room is lit by a few green lights, and tiny signs saying things like DANGER!, WARNING!, and HE OR SHE WHO HESITATES IS LOST! can be found around the room. On the far side, under an enormous porthole, is an enormous wooden table piled with books, maps, and dirty dishes.
At the top of a ladder rope running up the side of a wall in the Main Hall is the steering platform. On this small shelf are a large wheel and a few rusty levers and switches that seem to be incredibly difficult to understand.
Along a corridor of the Main Hall can be found the kitchen, the supply closet, and the barracks.
The crew of the Queequeg is required to wear a uniform that consists of:
- A bodysuit made of a shiny, sturdy waterproof material that is able to resist cooking spills, that has several loops around the waist, perfect for holding tools, and a waterproof pocket, perfect for holding a commonplace book, and that displays a portrait of Herman Melville on the front.
- Gloves made of the same waterproof material
- A diving helmet, large enough for a toddler to curl up in
In the book illustrations, the uniforms are blue. In the Netflix series, the uniforms are red.