Preheat oven to 400°F. Lightly grease a 9x13-inch baking dish with cooking spray and set aside.
Bring 12 cups water to a boil in a large pot. Once boiling, add 1 tablespoon fine sea salt and the ziti. Cook according to package directions, but reduce the cook time by 2 minutes. Drain and return pasta to the pot. Set aside.
Heat olive oil in a large nonstick pan over high heat. Add onion and sauté for 5-6 minutes. Push onion to the sides and add beef to the center. Let sear briefly, then crumble and begin cooking. While the beef cooks, add paprika, 1 tsp salt, 1 tsp pepper, onion powder, garlic powder, beef bouillon powder, sugar, and red pepper flakes if using. Continue cooking and crumbling until the beef is fully cooked through.
Add tomato paste, garlic, crushed fennel, basil, and oregano. Cook, stirring constantly, for 1 minute or until fragrant.
Reduce heat to low and stir in tomato sauce, crushed tomatoes, and Worcestershire sauce. Simmer 10 to 15 minutes, stirring occasionally, until slightly thickened.
While sauce simmers, freshly shred mozzarella and Parmesan cheese. Set aside. Open mascarpone.
Add 2-1/2 cups meat sauce to the cooked pasta and stir to evenly coat.
Spread half of the sauced pasta into the prepared baking dish. Dollop mascarpone evenly over the top. Sprinkle with 1/2 cup mozzarella and 1/2 cup Parmesan. Spoon 2 cups meat sauce over the cheese layer. Add the remaining pasta, then top with another 1/2 cup mozzarella, 1/2 cup Parmesan, and the remaining meat sauce.
Cover tightly with foil and bake for 10 minutes. Remove foil, sprinkle remaining 1/2 cup mozzarella on top, and bake another 10 to 15 minutes or until cheese is melted and edges are bubbling.
Let stand 5 to 10 minutes before serving. Top with extra Parmesan, fresh basil or parsley, and cracked black pepper if desired.
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Notes
Note 1: Mascarpone cheese is key to this recipe. Find it near the deli, dairy, or specialty cheeses. Ricotta works, but mascarpone is best!Note 2: Measure 2 teaspoons fennel seed into a plastic bag, then crush with a meat mallet or the bottom of a frying pan until powdery. A nut grinder also works.Storage: Store leftovers in the fridge for up to 4 days and reheat with a splash of broth if needed to bring back the sauciness. To make ahead, prepare the meat sauce, grate the cheese, and boil the pasta in advance, then store in the fridge separate. Assemble before baking and add 10 to 15 extra minutes to the covered bake time.ToFreeze: cook pasta slightly under al dente and toss with a little oil. Assemble with fully cooled layers, stopping before the final cheese topping. Cover tightly and freeze for up to 3 months. Thaw in the fridge for 24 hours, bake covered at 350°F for 25 minutes, then uncover, add cheese, and bake 10 minutes more. Thawing gives the best texture.