Heat 1 tablespoon of olive oil in a skillet over medium heat. Add the chopped onion and red bell pepper, sautéing until softened (about 5 minutes).
Stir in the minced garlic and cook for another minute until fragrant.
Add the tomato sauce or crushed tomatoes, thyme, oregano, salt, and pepper. Let simmer for 5 minutes. Spread this sauce evenly over the bottom of a round or oval baking dish.
Thinly slice the eggplants, zucchinis, yellow squashes, and tomatoes into rounds of similar thickness (about ⅛ to ¼ inch)
Arrange the slices in alternating patterns (e.g., eggplant, zucchini, squash, tomato) to form a circular or spiral pattern in the dish, starting from the outer edge and working inward. Slightly overlap the slices for a beautiful layered effect.
Drizzle the arranged vegetables with olive oil.
Sprinkle with additional thyme, oregano, salt, and pepper to taste
Cover the top of the dish with a piece of aluminum foil.
Bake in the preheated oven for 40–50 minutes, or until the vegetables are tender and slightly caramelized at the edges.
Remove the ratatouille from the oven and let it cool slightly.
Garnish with fresh basil leaves and an additional drizzle of olive oil before serving.
Notes
Uniform Slices: For even cooking, make sure all vegetable slices are of similar thickness.
Pre-Salt the Eggplant: To remove excess moisture and bitterness, sprinkle the eggplant slices with salt and let them sit for 10 minutes, then pat dry before layering.