Preheat and prep: Heat your oven to 375°F (190°C).
Lightly oil a 9x13-inch baking dish or similar casserole pan.
Cook the pasta: Boil in well-salted water until just shy of al dente (about 1 minute less than package directions). This prevents mushy pasta after baking. Drain and toss with olive oil.
Flavor the sauce (optional but great): In a skillet over medium heat, warm a drizzle of olive oil.
Add garlic for 30 seconds, then stir in marinara, Italian seasoning, and red pepper flakes. Simmer 3–4 minutes. Season to taste.
Combine: In a large bowl, mix pasta, most of the sauce (reserve 1/2 cup), half the mozzarella, half the Parmesan, and half the pepperoni.
Fold in any optional mix-ins. Adjust salt and pepper.
Assemble: Spread the reserved sauce over the bottom of the baking dish. Add the pasta mixture and smooth the top.
Sprinkle on the remaining mozzarella and Parmesan. Layer the rest of the pepperoni on top.
Bake: Cover loosely with foil and bake 15 minutes. Remove foil and bake another 8–12 minutes, until cheese is melted and bubbly and the pepperoni edges crisp slightly.
Finish: Let it rest 5–10 minutes so it sets and slices cleaner.
Garnish with chopped basil or parsley.
Serve: Spoon into bowls or cut into squares. Add a quick green salad or garlic bread if you like.