In a large casserole pan or dutch oven, heat 2 tablespoons of olive oil. When the oil is shimmering, add the chopped eggplant, zucchini, squash, and peppers and fry for about 5 to 8 minutes. Do this in batches so that the vegetables brown instead of steaming. Cook until they are golden and soft. Remove vegetables to a bowl.
In the same pan, add another 2 tablespoons of olive oil. Add the onions and cook for about 5 minutes. Add the garlic, basil stalks, and thyme and cook for another 5 to 7 minutes, or until vegetables are golden. Add salt and pepper.
Add the cooked vegetables back to the pan along with the raw tomatoes, plum tomatoes, balsamic vinegar, salt, and pepper.
Gently stir. Cover the pan and simmer over low heat for 40 minutes, or until reduced and sticky.
Adjust the seasonings. Grate the zest of 1/2 lemon and squeeze the juice over the ratatouille along with the remaining 2 tablespoons of olive oil.
Serve over rice, noodles, or as a spread on rustic bread.