Preheat your oven to 350°F. While it heats, gather all ingredients and measure them out—this ensures you won't scramble during assembly. Grease a 9x13 inch baking dish with a light coating of oil or cooking spray and set aside. Having everything prepped and ready will make the next steps flow smoothly without any rushed moments.
In a large skillet over medium-high heat, brown the Italian sausage, breaking it into small crumbles as it cooks (about 5-7 minutes until no pink remains). Simultaneously, bring a large pot of salted water to a boil and cook the mostaccioli for about 9 minutes—you want it slightly underdone since it will continue cooking in the oven. The pasta should have a slight firmness to it, not soft. Drain the pasta and set aside.
Add the marinara sauce and red pepper flakes to the cooked sausage in the skillet, stirring well to combine. Reduce the heat to low and let it simmer gently for 2-3 minutes so the flavors meld together. I like to taste the sauce at this point and adjust the seasoning if needed—it should be flavorful and balanced.
In a medium bowl, combine the cottage cheese, room-temperature eggs, 1/2 cup mozzarella, 1/3 cup Parmesan, fresh parsley, salt, and black pepper. Mix until everything is evenly incorporated and smooth. The room-temperature eggs blend much more easily with the cottage cheese, creating a creamier, more uniform filling without any lumps.
Spread half of the sausage-marinara sauce from Step 3 evenly across the bottom of your prepared baking dish. Layer half of the cooked pasta from Step 2 over the sauce, then spread the entire cottage cheese mixture from Step 4 in an even layer. Top with the remaining pasta, then finish with the rest of the sauce from Step 3. Sprinkle the 1 3/4 cups of freshly shredded mozzarella and 1/2 cup Parmesan evenly over the top.
Cover the baking dish tightly with aluminum foil and place it in your preheated 350°F oven. Bake for 30 minutes, then carefully remove the foil and bake uncovered for an additional 10 minutes, until the cheese topping is melted, bubbly, and lightly golden at the edges. The foil traps steam during the initial bake, keeping everything moist, while uncovering it at the end allows the cheese to brown beautifully.
Remove the mostaccioli from the oven and let it rest for 5-10 minutes before serving. This resting period allows the casserole to set slightly, making it easier to cut clean portions without the layers falling apart.