Jell-O® is made from gelatin, a processed protein that makes it wobbly. Gelatin is made from the collagen in cow or pig bones and skins. Gelatin melts when heated and solidifies when cooled again. When you add the Jell-O® powder to boiling water, the powder dissolves and the weak bonds that hold together the protein chains start breaking apart.
The chains float around in the mixing bowl until you add cold water. As the Jell-O® cools, the chains start bonding again. The chains become tangled when they are stirred, and water gets into gaps between the chains. Once it is refrigerated, the gelatin “chains” harden and the trapped water and flavor make Jell-O® wobbly.