1. Meanwhile, dice all the vegetables finely.
2. In a large pan or shallow pot or wok, heat oil and add onions. Sauté until translucent, and then add remaining vegetables.
3. Cook over medium heat, stirring occasionally to make sure the vegetables cook evenly. Cook until veggies are softening, about 10 minutes. Add the basil and marinara sauce.
4. Scrape out the flesh of the baked spaghetti squash with a fork, and set aside the shells for later use. Place spaghetti flesh into the vegetable mixture and mix all together to coat. Add salt and pepper to taste. I like to add a touch of sugar to counter the acidity.