Prepare the spaghetti squash according to the recipe.
Run a fork along the inside of the prepared squash to create spaghetti-like strands, scoop it into a medium-sized mixing bowl. Stir in basil and thyme then set aside.
Heat olive oil in large sauté pan over medium heat. Add onion and garlic, stirring frequently for 5 minutes, until onion begins to turn translucent. Add mushrooms, zucchini and green bell pepper. Sauté for 1 minute more then remove from heat.
Place half of the spaghetti squash in the bottom of a 2-qt casserole dish. Spread half of the sautéed vegetables over the squash then half of the marinara sauce over vegetables. Top with a layer of mozzarella cheese. Add the remaining squash. Layer the remaining vegetables then pour the remaining marinara sauce on top.
Mix the Parmesan cheese, mozzarella cheese and panko breadcrumbs together in a small bowl. Sprinkle over the entire dish.
Cover the dish with aluminum foil then bake for 20 minutes. Uncover and continue baking an additional 10 minutes or until hot and bubbly. Serve and enjoy immediately!
Notes
Need this dish to be gluten-free? Simply omit the panko!