Step 1: Preheat your oven to 375°F (190°C). Grease a 9×13 inch baking dish.
Step 2: Cook the ziti pasta according to package directions until al dente. Drain well and set aside.
Step 3: While the pasta cooks, prepare the marinara sauce. Heat olive oil in a large pot or Dutch oven over medium heat. Add chopped onion and cook until softened, about 5-7 minutes. Add minced garlic and cook for another minute until fragrant.
Step 4: Stir in the crushed tomatoes, tomato sauce, water (or broth), oregano, basil, and red pepper flakes (if using). Bring to a simmer, then reduce heat to low, cover, and let it cook for at least 15-20 minutes, stirring occasionally. Season with salt and pepper to taste.
Step 5: In a medium bowl, combine the cottage cheese, 1/2 cup Parmesan cheese, lightly beaten egg, and chopped fresh parsley (if using). Mix until well combined.
Step 6: In a large bowl, combine the cooked and drained ziti with about 3 cups of the marinara sauce. Toss gently to coat all the pasta. Reserve the remaining marinara sauce.
Step 7: Assemble the Cottage Cheese Baked Ziti with Marinara & Mozzarella: Spread a thin layer of the remaining marinara sauce on the bottom of the prepared baking dish. Spread half of the pasta mixture over the sauce.
Step 8: Evenly spread the entire cottage cheese mixture over the pasta layer.
Step 9: Top the cottage cheese layer with 2 cups of shredded mozzarella cheese.
Step 10: Add the remaining half of the pasta mixture over the mozzarella.
Step 11: Pour the rest of the marinara sauce over the top layer of pasta, ensuring it’s mostly covered. Sprinkle the remaining 2 cups of shredded mozzarella cheese evenly over the top.
Step 12: Bake for 25-30 minutes, or until the cheese is melted, bubbly, and lightly golden brown. If desired, you can broil for the last 1-2 minutes for an extra crispy top (watch carefully to prevent burning).
Step 13: Remove from the oven and let the Cottage Cheese Baked Ziti with Marinara & Mozzarella rest for 10-15 minutes before serving. This helps the layers set and makes for easier serving. Serve hot, garnished with extra fresh parsley or Parmesan cheese if desired.