Cut the peppers in half lengthwise. Scoop out and discard the seeds and membranes. Place the peppers skin side down in a 9 x 13 baking dish. Add enough water to cover the bottom of the pan. Bake for 10 minutes, then remove from the oven, leaving oven turned on.
Cut the pepperoni slices into quarters, reserving 12 whole slices for later.
Chop mushrooms, reserving 6 whole mushroom slices for later.
While peppers are baking, heat a large skillet over medium-high heat. Add the sausage, breaking up the lumps until the meat is cooked thru and just beginning to brown, 8 to 10 minutes. Remove to a paper towel-lined plate to absorb the fat.
Wipe out the skillet and add the pizza sauce, quartered pepperoni slices, chopped mushrooms and 1-1/2 cups mozzarella. Stir to combine. Add the sausage to the mixture and stir again until well combined.
Divide pizza mixture evenly among the pepper halves. Sprinkle over remaining cheese. Place 2 pepperoni slices and mushroom slice on top of the cheese.
Bake in preheated oven 20 to 25 minutes, until cheese is melted and starting to brown on top.