Preheat the oven to 350°F and spray a 13 x 9 inch baking dish with cooking spray.
Cook the spaghetti in salted boiling water, per the instructions on the box, until al dente. Do not overcook. Drain well.
On the stove top, in a medium sized pot, saute the diced onion, sliced green pepper and mushrooms in a couple of drizzles of olive oil or 2 minutes or until the onions turn translucent. Season with salt and black pepper, add garlic. Saute 1 minute..
Add ground beef and Italian sausage. Cook until no pink remains. Drain any excess fat from the pan, add Italian seasoning and red pepper flakes. Mix well.
Add tomatoes, tomato pasta, marinara sauce and 2 Tbsp parsley. Simmer covered for 30 minutes. Add 25 slices pepperoni at the end of cooking, mix well.
To assemble: Ladle 1/3 of the sauce into the bottom of the baking dish and cover with 1/2 of the cooked spaghetti.
Ladle another 1/3 of pasta sauce over the spaghetti, then sprinkle 1 cup of shredded mozzarella cheese, and 1/3 cup of grated Parmesan cheese.
Repeat, with the remaining spaghetti, then the final 1/3 of pasta sauce. Arrange 25 pepperoni slices over sauce.
Sprinkle the top with remaining mozzarella cheese and Parmesan cheese.
Bake for 30 minutes until the cheese is golden and bubbly. Cut and serve immediately.