Nelly Cootalot: The Fowl Fleet is a point and click adventure with a side view. The spirit of Captain Bloodbeard returns, mentioning that the main character did not understand the secret message from the last game, in which he sent Nellie to search for the treasure of the Seven Seas. She also learns that the captain's brother, Captain Broadbeard, was going to hypnotize thousands of birds so that they would follow his orders. Thus, Nellie has two tasks at once, because of which she has to escape from her home ship and begin her adventure immediately.