"He was right outside the door last night. Just staring and tapping at the wall. All I can think about since is that clanking of metal, those spidery legs, that face."

The Prototype is a towering mechanical-organic entity with a cracked porcelain jester face fixed in a wide, unnatural grin of square teeth. One eye socket is dark and hollow, while the other contains a small glowing orange mechanical pupil. He wears a worn, three-pronged jester hat with bell tips, along with a tattered blue coat and red bow. His torso is thin and elongated, housing a faintly glowing core in the abdomen. Long skeletal arms hang at his sides, ending in sharp articulated claws. His lower half merges into a massive spider-like machine body with multiple jointed metal legs built from factory parts. He also has three attached arms that are retractable in the abdomen of the spider-like machine body; one of Mommy Long Legs, one of Kissy Missy, and the other Huggy Wuggy. He has a body very similar to Doey's aggressive form, such as the 3 arms protruding from the front and a long torso with 6 legs. Also, he has purple fur his back and a red gas generator from Catnap. All which he most likely salvaged the spare parts of dead toys.

It was previously thought that, prior to The Hour of Joy, The Prototype was roughly the same shape and morphology as the person used to make him. It was not until Experiment 1160 that experiments were no longer bound to those rules regarding their shapes and sizes.[13][14] However, by the time the Player returns to the factory, it seems that 1006 may have grown in size. The Prototype presumably modified its current body from the spare parts of dead toys. As a result, he is not of human-scale, and is in fact enormous in proportion to the Player.