Puppeteer is a side-scrolling platformer in which players control a boy named Kutaro, who has been turned into a puppet and had his head torn off. Throughout the game, Kutaro is able to find various types of heads to substitute for his own, each with their own unique abilities, such as throwing bombs. Kutaro is armed with a pair of magical scissors named Calibrus. As well as serving as his main weapon, Kutaro can use the scissors to cut through and move along anything made out of paper or fabric, including effects such as bubbles and smoke that are made out of paper. The right analogue stick can be used to control Ying-Yang, a ghostly cat who can examine foreign objects and find new heads for Kutaro.