Cut Vegetables: Peel and cut eggplant into 1-inch cubes (Note 3). Cut onion into 1-inch pieces, and cut bell peppers into 1/2-inch pieces. Cut zucchini lengthwise into 6 long spears, then cut widthwise into 1/2-inch-thick pieces. Set aside.

Prepare Oven: Position oven rack in middle of oven, and preheat to 400 F.

Cook Aromatics: Add olive oil to large oven-safe pot (Note 4) over medium-high heat. Once heated, add onion, garlic, black pepper, and 1/2 teaspoon salt. Stirring occasionally, cook until onions are softened and browned, about 10 minutes. Stir in thyme and red pepper flakes for about a minute to release flavors. Add eggplant and tomatoes, briefly stirring until mixed.

Bake: Transfer pot to oven. Bake uncovered until eggplant is tender, about 35 minutes.

Let Stand: Remove pot from oven. Add bell peppers and zucchini, sprinkling 1/2 teaspoon salt on top, and briefly stir until mixed. Cover, and let stand until bell peppers and zucchini are tender, about 15 minutes (Note 5).

Finish & Serve: Uncover and stir in vinegar and basil. Loosen flavorful browned bits stuck to sides of pot, mixing them into ratatouille. Adjust salt and vinegar to taste. Transfer to platter or individual bowls, and serve (Note 6).