Heat olive oil in a large skillet over medium heat. Add the chopped onion and sauté until translucent, about 5 minutes, releasing a fragrant aroma.
Add the minced garlic to the skillet and cook for another 30 seconds until fragrant, stirring constantly to prevent burning.
Stir in the diced tomatoes, and cook for 8–10 minutes, stirring occasionally, until they break down and the mixture starts to thicken into a rich sauce.
Add the sliced zucchini, diced eggplant, and sliced bell pepper to the skillet. Mix well to coat the vegetables with the tomato sauce.
Sprinkle the dried thyme, salt, and pepper over the vegetables, then stir again to evenly distribute the seasonings.
Cover the skillet and reduce heat to medium-low. Let the vegetables simmer gently for about 20-25 minutes, stirring occasionally, until they are tender and flavors meld together.
Uncover and increase heat slightly to let any excess liquid evaporate, thickening the sauce and concentrating the flavors for about 5 minutes.
Taste and adjust seasoning if needed, then remove from heat. Garnish with chopped fresh basil if desired.
Serve the vegetable ratatouille hot, accompanied by crusty bread or as a side dish.