Melt bacon grease in a large cast iron skillet. Add onions and cook over medium heat until they are caramelized, about 20 minutes.
Spread onions evenly in the bottom of a greased 11×13 casserole dish.
Add half the zucchini rounds and lightly sprinkle with salt, pepper and thyme.
Repeat with squash and then tomatoes, seasoning each layer.
Add half the shredded cheese on top of the tomatoes.
Repeat the layering and seasoning with zucchini, squash and tomatoes. Add remaining cheese to the top of the casserole.
Bake uncovered in a 350 degree oven for 1 1/2 hours or until most of the liquid has evaporated.