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Preheat the oven to 375 degrees Fahrenheit. Brush a 9 x 13″ baking dish with olive oil.
Start a pot of well salted water to a boil. Boil the rigatoni until it is just al dente (start tasting a few minutes before the package recommends: you want it to be tender but still a little firm on the inside; usually around 7 to 8 minutes). Drain.
Meanwhile, mince the garlic. In a separate pot, heat the olive oil over medium high heat. Add the garlic and fennel seeds and cook for 1 to 2 minutes until fragrant. Add the basil, marinara sauce, and tomatoes and stir for 1 minute. Stir in 3/4 teaspoon kosher salt, 1/2 teaspoon onion powder and 1 pinch red pepper flakes and the 1/2 cup Parmesan cheese. Remove from the heat.
Pour the sauce and the drained pasta into the baking dish. Top with torn pieces of mozzarella. Sprinkle the entire top with generous sprinkles of Parmesan cheese.
Cover with foil and bake 15 minutes. Remove the foil and bake for an additional 10 minutes until browned.
Remove the pan from the oven and top with 1/4 teaspoon kosher salt, divided over the top. Let stand 5 minutes. If desired, garnish with chopped basil. (Make ahead instructions: Make the pasta through Step 4 and cover with foil. Refrigerate until baking, up to 24 hours.)