Preheat the oven to 375°F.
Meanwhile, poke several holes in the spaghetti squash using a fork. Then, microwave it until it becomes slightly tender, about 4-6 minutes.
Slice squash in half and remove the seeds and membranes.
Place halves, sliced side up, on a nonstick baking tray, and brush the tops with olive oil.
Roast it in the oven for about 40-50 minutes or until the squash is fork-tender.
While roasting, make the marinara sauce. In a saucepan, sauté onions and garlic in olive oil over medium-high heat. Add in the tomatoes and water, and simmer for 30 minutes. Add in the remaining ingredients and season with salt and pepper to taste.
Transfer to a blender or food processor and purée until smooth. Set aside.
Check out the squash and once it’s cooked, remove it from the oven and set aside to cool.
Shred the squash into a large bowl using a fork. Toss with the marinara sauce.
To serve, divide the squash spaghetti into four plates then sprinkle with red pepper flakes and black pepper.