Preheat the oven to 375°F (190°C).
Bring a large pot of salted water to a boil. Add the ziti pasta and cook until al dente, about 8 minutes. Drain and set aside.
Heat olive oil in a large skillet over medium heat. Add the chopped onion and cook until softened, about 5 minutes.
Add the minced garlic and cook for 1 minute until fragrant.
Stir in the crushed tomatoes, dried oregano, dried basil, red pepper flakes, salt, and black pepper. Simmer the sauce for 15 minutes, stirring occasionally.
In a large mixing bowl, combine ricotta cheese, 1 cup of shredded mozzarella, 1/2 cup of grated Parmesan, and the egg. Mix well.
Add the cooked pasta to the tomato sauce and stir to combine evenly.
In a 9×13 inch baking dish, spread half of the pasta and sauce mixture.
Drop spoonfuls of the ricotta cheese mixture evenly over the pasta layer.
Top with the remaining pasta and sauce mixture.
Sprinkle the remaining 1 cup mozzarella and 1/2 cup Parmesan cheese evenly on top.
Cover the baking dish tightly with aluminum foil and refrigerate if preparing ahead. When ready to bake, remove from refrigerator and let stand at room temperature for 20 minutes.
Bake covered for 25 minutes. Remove the foil and bake for an additional 15 minutes or until the cheese is bubbly and golden brown.
Let the baked ziti rest for 10 minutes before serving.
Garnish with chopped fresh basil leaves if desired.