Begin by making the marinara sauce: In a large skillet, over medium heat, cook the onion and garlic in the olive oil, until the onion is softened.
Add the strained tomatoes, tomato paste, chicken stock, sugar, oregano, salt, cubanelle pepper and red pepper flakes. Simmer uncovered for thirty minutes. Reserve one cup of sauce for another use.
Preheat the oven to 350 degrees.
Cook the noodles according to the package directions for al dente noodles.
In a large bowl, mix together the ricotta, basil and egg.
Next, heat a large skillet on medium heat. Melt the butter and cook the mushrooms and peppers until the mushrooms start to brown.
In a deep 13x9 baking dish, place a layer of noodles. Top with a quarter of the sauce, and then a quarter of the ricotta, and a quarter of the mozzarella. Repeat this three times. Add a layer of Parmesan cheese. Finally, add the mushrooms, peppers, and pepperoni.
Bake uncovered for thirty minutes. Sprinkle with basil leaves and serve.