Fat Cook is a puzzle-platformer that follows the adventures of a brave man on a mission to cook a meal that will save all of mankind. The Chef must roam the empty City using his jumping skills and wits in order to collect all of the ingredients written down on a mysterious letter he found in the basement of his restaurant.

On the night when the Cook falls through the floor of his restaurant, he finds a letter that predicts his fall and the situation that surrounds him. The author of the letter is surprisingly aware that the city streets are abandoned, and that many people have turned into cyborgs. The author, who appears to be the Cook's friend, sends him of to a quest to find the ingredients of a secret recipe that will help save him and all of mankind.

Throughout the game, Cook reveals other letters that his unnamed friend has left him. They contain clues which guide him to hidden ingredients that he needs to collect in order to prepare the secret recipe. However, these ingredients aren't the only things he discovers. After many surprises and adventures, the Cook solves the biggest mystery - the identity of the "Friend" and how he came to know what lies in the future.