Sauté onion slices in 1 tablespoon olive oil, lower heat until caramelized, and season with salt and pepper.
Brush the bottom of a deep dish pie pan with olive oil. Layer the pan with half of the zucchini slices. Sprinkle zucchini with salt, pepper, thyme, and olive oil. Layer sautéed onions on top of zucchini, then follow with the tomato slices. Sprinkle with salt and pepper. Layer final half of zucchini on the tomatoes. Sprinkle with salt, pepper, thyme, olive oil, and Parmesan cheese.
Bake at 425 degrees until lightly browned on top, approximately 40 minutes. Enjoy.