Poke spaghetti squash all over with a knife and cook in the microwave for eight to 12 minutes until soft. If you don't have a microwave, place the poked squash on a baking pan and bake at 375ºF for 45 to 60 minutes. While that's cooking, add the oil, garlic, pepper, courgette, and carrots to a pan, cooking over medium heat.
Cut the squash in half, scoop out the seeds, and with a fork, scrape the flesh from the peel. It should flake off easily in strings, resembling spaghetti. Place the spaghetti squash flesh in a casserole dish. Add the cooked veggies, diced tomato, sauce, and most of the cheese and mix well. Sprinkle leftover cheese on top and bake for 30 minutes or until the cheese is bubbly.