Preheat the oven to 350 degrees F.
Render bacon in a large skillet over medium heat. Transfer the cooked bacon to a paper towel lined plate. Add the bread crumbs to a small bowl. Remove 2 tablespoons of the bacon fat from the skillet and stir into the bread crumbs. Add the onion rounds to the skillet in batches and cook, without breaking the round slices apart, until there is some golden color, about 5 to 6 minutes per side.
To assemble the gratin, overlap the green tomato slices in 1 row in a large baking dish, about 9 by 11 inches. Next, make a row slightly overlapping of the partially cooked onion rounds, being careful to keep the slices intact. Repeat steps until all tomatoes and onions are used. Season tomatoes and onions lightly with salt and heavily with pepper. Crumble the bacon over the vegetables; sprinkle the grated Cheddar over the top followed by the bread crumbs. Bake until the cheese is bubbly, about 30 to 45 minutes. If the top is getting too brown, loosely cover with foil.