Preheat the oven to 350°F. Combine the rice and the water in a small saucepan and bring it to a boil. Cover and simmer on low heat for 20 minutes. While the rice is simmering, cook the ground beef with the onions in a large skillet. Drain any excess grease, if needed.
Add the mushrooms, spaghetti sauce, Worcestershire sauce, garlic powder, onion powder, salt, pepper, Italian seasoning, and red pepper flakes to the skillet with the meat. Bring to a simmer and cook for about 5 minutes.
While the filling is simmering, split the peppers in half and remove the seeds. Place the peppers on a large sheet pan and set aside. Add the cooked rice to the skillet with the meat and sauce. Stir to combine.
Spoon an equal amount of this mixture into each bell pepper. Pour the remaining spaghetti sauce over the top of each pepper.
Cover loosely with foil and bake 50 minutes in the oven. Remove foil and top with cheese. Place back in the oven just until the cheese is melted, approximately 10 minutes. Sprinkle with parsley before serving.