Preheat oven to 375°F (190°C).
In a skillet, heat 1 tablespoon of olive oil and sauté onion and garlic until softened.
Add crushed tomatoes, thyme, basil, salt, and pepper. Let simmer for 10 minutes to create a base sauce.
Spread the sauce evenly in the bottom of a baking dish.
Arrange the sliced vegetables on top in an overlapping spiral pattern.
Drizzle the remaining olive oil over the vegetables.
Cover with foil and bake for 30 minutes.
Remove foil and bake for another 15 minutes until vegetables are tender.
Garnish with fresh basil before serving.