01 - Preheat oven to 400°F. Cut squash lengthwise, scoop seeds, brush cut sides with 1 tbsp olive oil and season. Place cut-side down on parchment-lined baking sheet. Roast 35-40 minutes until tender.
02 - While squash roasts, heat remaining oil in large skillet over medium heat. Cook sausage, breaking up with spoon, until browned, about 6-7 minutes.
03 - Add onions and bell peppers to sausage. Sauté 5 minutes until softened. Stir in garlic, oregano, basil, and red pepper flakes; cook 1 minute more.
04 - Pour marinara sauce into skillet. Simmer 5 minutes then remove from heat.
05 - When squash is cool enough to handle, use fork to scrape flesh into spaghetti-like strands. Discard skins. Reduce oven temperature to 375°F.
06 - In large mixing bowl, combine squash strands, sausage mixture, half the mozzarella, and half the Parmesan. Mix well and season to taste.
07 - Transfer mixture to greased 9x13-inch baking dish. Top with remaining cheeses. Bake uncovered 15-20 minutes until bubbly and golden. Rest 5 minutes before serving with fresh basil.