Step 1: Preheat your oven to 375°F (190°C). Bring a large pot of salted water to a rolling boil. If salting your eggplant, do so now (toss cubes with 1 tsp salt, let sit 30 mins, then rinse and pat dry) and let it sit while you prep other ingredients.
Step 2: Heat the olive oil in a large oven-safe pot or Dutch oven over medium heat. Add the chopped onion and cook until softened and translucent, about 5-7 minutes.
Step 3: Add the minced garlic and cook for another minute until fragrant, being careful not to burn it. Then, add the cubed eggplant and bell peppers. Sauté for 8-10 minutes, stirring occasionally, until the vegetables begin to soften and lightly brown.
Step 4: Stir in the zucchini and continue to cook for another 5 minutes until it starts to soften.
Step 5: Pour in the crushed tomatoes, vegetable broth, dried oregano, dried thyme, and bay leaf. Season generously with salt and black pepper. Bring the mixture to a simmer, then reduce heat to low, cover, and let it cook for at least 15-20 minutes, allowing the flavors to meld.
Step 6: While the sauce simmers, cook your pasta in the boiling salted water according to package directions until it’s al dente – slightly firm to the bite. Drain well.
Step 7: Remove the bay leaf from the sauce. Stir in the cooked pasta and most of the fresh basil and fresh oregano. Taste and adjust seasonings as needed. If using a separate baking dish, transfer the pasta and vegetable mixture to it now.
Step 8: Sprinkle the shredded mozzarella and Parmesan cheese evenly over the top of the Ratatouille Baked Pasta.
Step 9: Bake uncovered for 20-25 minutes, or until the cheese is bubbly and golden brown, and the sauce is simmering. For an extra crispy top, you can broil for the last 2-3 minutes, watching carefully to prevent burning.
Step 10: Carefully remove the dish from the oven. Let it rest for 5-10 minutes before serving to allow the sauce to set. Garnish with the remaining fresh basil and a drizzle of good quality extra virgin olive oil. Serve hot.