Prepare the Sauce: Heat two tablespoons of olive oil in a large oven-safe skillet or a separate pan. Add the diced onion and red bell pepper. Sauté until they soften and start to brown. Stir in the minced garlic and cook for one more minute.

Simmer the Base: Pour the crushed tomatoes into the skillet. Add the dried oregano, salt, pepper, and balsamic vinegar. Let the sauce simmer on low heat for about ten minutes.

Slice the Vegetables: While the sauce simmers, slice your zucchini, yellow squash, eggplant, and Roma tomatoes into thin rounds, about 1/8 inch thick.

Arrange the Veggies: Spread the sauce evenly across the bottom of your baking dish. Start layering the vegetable slices in an alternating pattern.

Finish the Pattern: Continue the spiral pattern until you reach the center of the dish. Pack the slices tightly.

Season and Oil: Mix the remaining olive oil with fresh thyme and minced garlic. Drizzle this mixture over the top. Season generously with salt and pepper.

Bake Covered: Cover the dish with parchment paper or foil. Bake at 375°F for about 40 minutes.

Bake Uncovered: Remove the cover and bake for another 20 minutes.

Garnish and Serve: Let it rest for five minutes and garnish with fresh basil leaves before serving.