Preheat oven to 375 degrees F. 

Heat olive oil in a large oven safe pan. Add the onion, garlic, and bell pepper and sauté till softened. Add the salt, pepper, oregano, red pepper flakes, and thyme. Add the crushed tomatoes and fresh basil. 

Let sauce simmer for 20-35 minutes to let flavors combine. Spread sauce with a spatula to smooth it out. 

In a large bowl make the herb topping by combining the basil, garlic, salt, pepper, and olive oil. Add the sliced eggplant, tomatoes, squash, and zucchini and toss to coat them in the topping.

Arrange the seasoned vegetable slices alternating the vegetables (eggplant, tomato, squash, zucchini) on top of the sauce. Work from the outer edge of the pan inward. 

Cover the pan with foil and bake for 40 minutes. Uncover and bake for another 20 minutes until the vegetable are softened. 

Top with more fresh herbs or parmesan cheese and enjoy!