The Great Unknown is a mysterious question mark shaped object that roams about the sea. Jacques Snicket was the very first to refer to it as "The Great Unknown."
For obvious reasons, not much is known about The Great Unknown, except that it slithers about like a snake. It appears to look like a "shadow as chilling as Count Olaf's glare and as dark as villainy itself." It is larger than The Carmelita and The Queequeg. There is no proof of, or even a hint at, what could be lying underneath the waters where the question mark roams.
It is also unknown whether The Great Unknown is evil or noble. Captain Widdershins said that the question mark "was something even worse than Olaf himself," and Snicket describes its aura of menace. Even Count Olaf himself fears the object. Yet, when Kit Snicket was aboard the Queequeg at the time that it was first approached by the question mark, the crew of the submarine decided to take their chances with it; it is unknown what happened to them.
The picture at the end of The End suggests that Violet, Klaus, Sunny, and Beatrice Snicket encountered The Great Unknown, due to a question mark that can be seen in the water. It is left a mystery as to what happened to them as well.