Start by heating 1 tablespoon of olive oil in a large oven-safe skillet over medium heat. Add the chopped onion and sauté until it turns translucent, about 3–4 minutes. Stir in the minced garlic and cook for another minute until fragrant.
Pour in the crushed tomatoes, then season with thyme, oregano, salt, black pepper, and red pepper flakes. Let the sauce simmer for about 10 minutes, allowing the flavors to meld together
While the sauce simmers, preheat your oven to 375°F (190°C). Arrange the sliced vegetables in an alternating pattern (eggplant, zucchini, yellow squash, bell peppers, and tomatoes) on top of the tomato sauce.
Start from the outer edge and work your way toward the center in a circular pattern for a visually stunning presentation.
Drizzle the remaining olive oil over the vegetables and sprinkle a little extra thyme and oregano for added flavor. Cover the skillet with aluminum foil and bake for 35 minutes.
Then, remove the foil and bake for an additional 15 minutes until the vegetables are tender and slightly caramelized.
Once the ratatouille is out of the oven, let it cool for a few minutes before garnishing with fresh basil leaves.