01 - Preheat oven to 400°F. Line a baking sheet with parchment paper. Cut spaghetti squash in half lengthwise and scoop out seeds. Brush cut sides with 1 tablespoon olive oil and season with salt and pepper. Place squash halves cut-side down on prepared baking sheet.
02 - Roast squash for 35 to 40 minutes until tender and strands easily pull away with a fork.
03 - While squash roasts, heat remaining olive oil in a large skillet over medium heat. Add sausage and cook, breaking up with a spoon, until browned and cooked through, about 6 to 7 minutes.
04 - Add onions and bell peppers to the skillet. Sauté for 5 minutes until softened. Stir in garlic, oregano, basil, and red pepper flakes. Cook 1 minute more until fragrant.
05 - Pour marinara sauce into the skillet. Simmer for 5 minutes to combine flavors, then remove from heat.
06 - Once squash is cool enough to handle, use a fork to scrape flesh into spaghetti-like strands. Discard the skins. Reduce oven temperature to 375°F.
07 - In a large mixing bowl, combine squash strands, sausage mixture, half the mozzarella, and half the Parmesan. Mix well and season to taste.
08 - Transfer mixture to a greased 9x13-inch baking dish. Top with remaining mozzarella and Parmesan cheeses.
09 - Bake uncovered for 15 to 20 minutes until cheese is melted, bubbly, and golden brown.
10 - Let casserole rest for 5 minutes before garnishing with fresh basil and serving.