Preheat oven to 375°F (190°C).
Bring a large pot of salted water to a boil. Cook the ziti pasta according to package instructions until al dente, about 8 minutes. Drain and set aside.
In a large skillet, heat olive oil over medium heat. Add minced garlic and cook until fragrant, about 1 minute. Remove from heat.
In a large mixing bowl, combine ricotta cheese, eggs, half of the shredded mozzarella, grated Parmesan, chopped basil, salt, black pepper, and crushed red pepper flakes. Mix well.
Add the cooked pasta, marinara sauce, and garlic with olive oil to the cheese mixture. Stir gently until all ingredients are evenly combined.
Lightly grease a 9×13 inch baking dish. Pour half of the pasta mixture into the dish and spread evenly.
Sprinkle half of the remaining mozzarella cheese over the pasta layer.
Add the remaining pasta mixture on top and spread evenly.
Top with the remaining mozzarella cheese.
Cover the baking dish tightly with aluminum foil.
Bake in the preheated oven for 30 minutes.
Remove the foil and bake for an additional 15 minutes, or until the cheese is bubbly and golden brown.
Remove from oven and let stand for 10 minutes before serving.