Heat large oven-proof skillet or dutch oven over medium-high heat. Add 1 Tablespoon oil and heat until shimmering.
Add the chicken and cook until browned on all sides, stirring occasionally., about 4 minutes. Sprinkle with salt and pepper. Chicken may not be fully cooked at this point. Remove from pan and set aside.
In the skillet , over medium-high heat, heat the remaining 1 Tablespoon oil. Add the green peppers, onions and pepperoni quarters. Cook, stirring occasionally until the green peppers and onions are softened and the pepperoni starts to crisp, about 4 minutes. Add back in the chicken.
Sprinkle the Italian seasoning, oregano and red pepper flakes into the skillet. Stir to combine and cook 1 minute.
Into the skillet, add the marinara sauce, garlic, pasta and water. Stir to combine. Bring the mixture to a boil, then cover and reduce heat to simmer for 15 minutes or until noodles are cooked al dente. Add additional water 1/4 cup at a time, if mixture gets too thick and pasta is not done.
Preheat the boiler.
Remove the skillet from heat. Sprinkle the cheese evenly over the pasta mixture. Distribute 12 reserved pepperoni slices over the top.
Place the skillet under the broiler for 2 minutes until the cheese is melted and golden brown.
Garnish with basil and serve hot.