Step 1

Preheat the oven to 375°F.

Step 2

In a large skillet pan, heat 1 tablespoon of the oil over medium heat. Add the onion, bell pepper, ¾ teaspoon of the salt, and ½ teaspoon of the black pepper, and cook, stirring frequently, until the onion is soft and lightly golden, 5 to 7 minutes. Add the garlic, and cook until fragrant, about 1 minute. Add the crushed tomatoes, and bring to a gentle simmer. Reduce the heat to medium-low and simmer until slightly reduced, about 5 minutes. Remove the sauce from the heat and stir in 1 teaspoon of the thyme. Spoon the sauce into a 2-quart casserole dish.

Step 3

Using a sharp knife or serrated knife, slice the tomatoes and eggplant into ⅛-inch-thick slices. Use a sharp knife or a mandoline to slice the zucchini and yellow squash into ⅛-inch-thick slices.

Step 4

Shingle the sliced vegetables on top of the sauce in an alternating pattern, working from the outer edge to the center of the dish. Brush 2 tablespoons of the oil on the vegetables and sprinkle with the remaining 1 teaspoon thyme,  ½ teaspoon salt, and ½ teaspoon black pepper.

Step 5

Cover the dish with parchment paper or aluminum foil, and bake for 45 minutes. Uncover the dish, and bake until the vegetables are tender and lightly golden, about 20 minutes more.

Step 6

Allow the dish to cool for 5 minutes. Drizzle with the remaining 1 tablespoon oil, and serve hot or warm, sprinkled with basil.