Place your oven rack in the middle position, and preheat the oven to 450 degrees F. Spread the marinara sauce on the bottom of a 9x13-inch dish.
Place the Parmesan in a separate shallow dish. Sprinkle the chicken with salt and pepper, then roll in the Parmesan and coat completely (pat it on so it will stick well). Lay the coated chicken in the marinara sauce dish. Maybe sprinkle a little more Parmesan on top! Bake for 15 minutes.
While the chicken is baking, prepare the pasta. Cook the spaghetti according to package instructions. Reserve 1/4 cup of the pasta water. Drain the pasta, then return the pasta to the pot along with the pasta water.
Remove the pan from the oven. Sprinkle mozzarella on top. Spread out the pepperoni slices over the top of the cheese. Increase the oven temp to 475 and continue to bake until the cheese melts and the chicken registers 160 degrees, 5 to 7 minutes longer.
Spoon some of the sauce from the pan with the chicken in it into the pasta. Stir until coated. Plate four dishes with pasta and top with some of the chicken and more sauce.