Preheat your oven to 375°F (190°C).
Cook the rotini pasta in a large pot according to package instructions until al dente. Drain and set aside.
In the same pot, brown the ground beef and Italian sausage over medium heat until fully cooked, breaking up any large pieces. Drain excess fat.
Add diced onion and minced garlic to the meat mixture, cooking until the onion is soft, approximately 3-5 minutes.
Stir in the pizza sauce, cooked pasta, pepperoni slices, Italian seasoning, and season with salt and pepper to taste. Mix thoroughly to combine.
Transfer half of the meat and pasta mixture into the baking dish. Spread 1 cup of mozzarella cheese over the top.
Add the remaining pasta mixture on top and finish with the remaining mozzarella and cheddar cheese.
Cover the baking dish with aluminum foil and bake in the preheated oven for 25 minutes.
Remove the foil and bake for an additional 15 minutes, or until the cheese is bubbly and golden.
Once baked, let it cool for 5 minutes before serving. Garnish with fresh basil if desired.