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.
In a large skillet, heat olive oil over medium heat. Add the chopped onion and sauté until translucent, about 5 minutes.
Add the minced garlic and cook for 1 minute until fragrant.
Pour in the crushed tomatoes, then stir in dried oregano, dried basil, red pepper flakes, salt, and black pepper. Simmer the sauce for 15 minutes, stirring occasionally.
Remove the sauce from heat and stir in chopped fresh parsley.
In a large bowl, combine ricotta cheese, eggs, and grated Parmesan cheese. Mix well.
Add the cooked ziti pasta to the ricotta mixture and stir until evenly coated.
Add half of the tomato sauce to the pasta and ricotta mixture and gently fold to combine.
Spread a thin layer of tomato sauce on the bottom of a 9×13-inch baking dish.
Pour half of the pasta mixture into the baking dish and spread evenly.
Sprinkle 2 cups of shredded mozzarella cheese over the pasta layer.
Add the remaining pasta mixture on top and spread evenly.
Pour the remaining tomato sauce over the top layer.
Sprinkle the remaining 2 cups of shredded mozzarella cheese evenly over the top.
Cover the baking dish tightly with aluminum foil and refrigerate if making ahead, up to 24 hours.
When ready to bake, preheat the oven to 375°F (190°C). Bake the covered dish for 25 minutes.
Remove the foil and bake for an additional 15 minutes until the cheese is bubbly and golden.
Let the baked ziti rest for 5 minutes before serving.