The name of the ship is taken from as a character in Moby Dick by Herman Melville.
Violet, Klaus, and Sunny Baudelaire were rescued by the captain and his crew after being washed down the river from the Mortmain Mountains. Later, an unknown scribble and an octopus looking figure appeared on the sonar screen. The octopus figure turned out to be Count Olaf, while the scribble, 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 Baudelaires 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. It is assumed that the submarine was abandoned there. Lemony Snicket mentioned that, because he misread a group of sausages as spelling a K rather than an R, he caused the loss of an important bathyscaphe, possibly referring to the Queequeg.
The Queequeg sailed out to sea to find the self-sustaining hot air balloon. After reuniting on Hector's float, they were attacked by trained eagles, which took out their balloon, causing them to crash the Queequeg and destroying it. There, they were taken by the mysterious object shaped like a question mark which they had encountered earlier in The Grim Grotto.
Years later, Lemony Snicket would conduct his investigation of the Baudelaire's time in the submrine (recorded in The Grim Grotto) at its remains.
The boat had a "Crew of Two," originally consisting of Captain Widdershins and Fiona's mother. After her death, her position was filled, at different times, by Jacques Snicket, Lemony Snicket, and a woman who turned out to be a spy. At the time of the Baudelaire's arrival, Phil, formerly of Lucky Smells Lumbermill, was working as the submarine's cook. Widdershins's stepdaughter Fiona, fills the important role of chief engineer of the submarine, but is never considered to be part of the crew.
It is said that Kit Snicket helped in the construction of the Queequeg. When the Baudelaires happened upon it, the Queequeg was in a state of extreme disrepair. Apparently there were many leaks in the ship, and several of the rooms had to be closed off to avoid the ship's sinking.
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; boots; and a diving helmet.