Puppeteer is an action-adventure game where Kutaro, a young boy, must escape the evil Moon Bear King's castle after being taken away. With the help of a mysterious flying cat and magic scissors called Calibrus, Kutaro must navigate through the castle and rescue his fellow comrades. The gameplay involves side-scrolling platforming in both 2D and 3D environments, with puzzle-solving elements based on picking up and carrying multiple replacement heads. Losing a head causes Kutaro to lose health, so it's essential to pick it up quickly before it disappears. Collecting 100 moonsparkles provides extra lives.
Players control both Kutaro and his companion simultaneously using an analog stick for each character. The game supports two players, with the second player controlling the companion. Companions can examine objects, pick up moonsparkles, and heads, adding to the gameplay experience.
Puppeteer is presented as a puppet show with seven acts and three levels each, featuring different companions that can aid in the gameplay.