When Puppeteer begins, Kutaro finds himself in the clutches of the evil Moon Bear King. He must escape the castle and rescue his fellow companions to break free from the king's grasp. With the help of a mysterious flying cat and magical scissors called 'Calibrus', Kutaro will have to navigate through various challenges.
The game allows for simultaneous control of Kutaro and his companion using an analog stick for each character. The second player's role is supported, with companions having their own abilities, such as examining objects, picking up moonsparkles, and heads. Puppeteer features seven acts, divided into three levels per act.