Prototype made his first proper appearance in Poppy Playtime Chapter 3, or his arm did. So far, the name Prototype is associated with only a bony, skeletal arm with a single human muscle.

but we may have a solid clue about who the villain is in Poppy Playtime Chapter 4. Chapter 3 ended with the death of CatNap, the main antagonist who worshiped the mysterious Prototype. Now ...