Cook the gound beef in a medium skillet with the onions, green peppers, garlic, salt pepper until meat is browned and veggies are tender; drain fat, and mix in the Parmesan cheese.
Stir in the 1/2-pound pepperoni (chop this pepperoni to add to the mixture, leave the remaining half pound pepperoni sliced), mushrooms, pasta sauce; stir well until combined; simmer for 20-25 minutes on top of stove.
Set oven to 350 degrees.
Place the cooked rigatoni pasta on the bottom of the greased baking dish.
Sprinkle with 2 cups mozzarella cheese over the pasta.
Layer with pepperoni slices evenly over the cheese.
Top with the ground beef/pasta sauce mixture.
Bake uncovered for 30 minutes.
Remove from oven, sprinkle with the remaining 2 cups mozzarella cheese.
Return to oven and bake for 10 minutes longer, or until bubbly.