Preheat the oven to 400ºF. Place the peppers cut side up onto the baking dish and bake for about 20 minutes.
Meanwhile, in a heavy pan, heat the oil on medium-high heat. Add the onions and mushrooms, stir, and cook for about 7-8 minutes.
Add the steak to the pan and cook for 3-5 minutes, until just done and no pink color remains. Season with salt, pepper, and red pepper flakes. Stir and remove the pan from the heat.
Place a spoonful of rice inside each pepper half (the amount of rice depends on the size of your peppers). Add a half slice of cheese on top.
Fill each pepper with the cheesesteak mixture. Add another half slice of cheese on top of each pepper.
Bake for about 5-7 minutes, just until the cheese melts nicely. Garnish with freshly chopped parsley and serve.