Quarter half of the pepperoni slices and keep the rest whole for the topping. The smaller pieces melt into the sauce, while the full slices stay visible on top after broiling.
Set a Dutch oven or deep pot over medium-high heat, add a light drizzle of olive oil, and cook the Italian sausage for 4 to 5 minutes, breaking it into small crumbles as it browns; then drain off the excess grease and return the sausage to the pot. The sausage should lose its raw look and pick up browned edges, and draining now keeps the finished pasta from tasting oily.
Stir in the cut pepperoni, diced onion, and diced green pepper and cook for about 3 minutes, then add the garlic and cook for 30 seconds more. The vegetables should start to soften, and the garlic and herbs will smell especially fragrant once the garlic hits the heat.
Add the marinara sauce, oregano, and basil, then pour in the water and bring everything to a boil over high heat before stirring in the dry pasta. Once the pot boils, the liquid should look well combined and ready to cook the pasta evenly.
Reduce the heat to a simmer, cover, and cook for 12 to 15 minutes, stirring a few times as it cooks. The pasta should become tender and the sauce should thicken noticeably as the starches release, with most of the extra liquid absorbed by the end.
Take the pot off the heat, stir in 1 cup of mozzarella cheese, and season with salt and pepper to taste, then scatter the remaining mozzarella over the top and arrange the reserved pepperoni slices over the cheese. The stirred-in cheese should make the sauce look glossier and a little thicker before the topping goes on.
Broil on high for 1 to 3 minutes until the cheese is melted, bubbly, and lightly golden, then finish with fresh minced parsley or basil. Watch closely here, because the top can move from beautifully bronzed to burnt very quickly under the broiler.