Preparing the Ingredients: Preheat oven to 400°F (200°C). Toss diced butternut squash with 1 tablespoon olive oil, salt, and pepper. Roast on a baking sheet for 20 minutes until tender and lightly caramelized. Cook ziti pasta according to package instructions until al dente. Drain and set aside.
Cooking the Sausage Mixture: In a large skillet, heat 1 tablespoon olive oil over medium heat. Add Italian sausage and cook, breaking it up, until browned and cooked through. Add chopped onion and garlic; sauté 3–4 minutes until fragrant and softened. Stir in marinara sauce, oregano, and red pepper flakes. Simmer 5 minutes.
Assembling the Baked Ziti: In a large mixing bowl, combine cooked pasta, roasted butternut squash, sausage mixture, and ricotta cheese. Mix gently. Transfer to a greased 9x13-inch baking dish. Sprinkle shredded mozzarella and grated Parmesan evenly on top.
Baking: Cover with foil and bake in preheated oven for 20 minutes. Remove foil and bake for an additional 10–15 minutes until cheese is golden and bubbly. Let stand 5 minutes before serving.