Place 1 tablespoon of the olive oil in a large sauté pan over medium-high heat. Add the onions and sauté for about 5 minutes, or until the onions are translucent and fragrant. Add the bell peppers and sauté for another 5 minutes, or until the peppers begin to soften. Add the garlic and cook for about 2 minutes more, or until the garlic becomes fragrant. Transfer the sautéed onions, peppers and garlic to a bowl and set aside.

Return the pan to medium-high heat and add another tablespoon of olive oil. Add the zucchini and/or yellow squash to the pan and cook for about 5-7 minutes, or until the squash becomes tender. Remove the squash and reserve in the same onion pepper bowl.

Return the pan to medium-high heat and add the remaining tablespoon of olive oil. Add the eggplant and sauté for 2 minutes. Add the water to prevent the eggplant from burning after it absorbs the olive oil. Cook the eggplant for 5 minutes more, or until the water has absorbed and the eggplant has softened, adding additional olive oil or water if the eggplant begins to burn.

Add the tomatoes to the sauté pan with the eggplant. Cook for about 2-3 minutes, or until the tomatoes begin to break down and the eggplant is soft. Add the reserved onions, bell peppers and squash back to the pan, folding all ingredients together evenly with a wooden spoon.

Cook for 5 minutes more and add the basil and thyme. Season with salt and pepper to taste, divide into 6 portions and enjoy!