Fill a 6-quart pot ⅔ full with hot water. Place over high heat on the stove and cover.
Rinse your peppers and pat them dry. Cut out the stems and slice each pepper in half. Scrape out the seeds and membranes and discard them.
When your water is boiling, carefully place the pepper halves in the pot. Boil the peppers for three minutes.
Carefully drain the peppers in a colander in the sink. Use tongs to turn the peppers so the cut sides face down, allowing the water to drain out of them. Let them sit in the colander as you make your meat filling.
Peel your onion and chop it. Preheat your oven to 375 degrees F. Grate your Pecorino and shred your mozzarella, if needed.
Add your ground beef to a 12-inch skillet on the stove over medium-high heat. Break up the meat with a wooden spoon. After a minute, stir in the chopped onions, red pepper flakes and salt. Cook, stirring frequently, until the meat is browned and the onions are tender. If your meat is lean enough (90%) you shouldn't have to drain any fat. If you have lots of liquid, drain most of it.
Stir in 1 ½ cups of marinara sauce to the meat mixture. Stir in the rice (if it was frozen, thaw it in the microwave first.) Add the Pecorino Romano and stir to combine. Cook the mixture for a couple minutes, or until it's heated through.
Prepare a half sheet pan or a 10x15 baking pan for the peppers. If using a sheet pan, line it with foil and grease it with cooking spray. If using a 10x15 pan, just grease it with spray.
Add your drained pepper halves to your baking pan, cut side up. Scoop about three tablespoons of the meat filling into each pepper half. Add more meat as needed, until each pepper half is filled to the surface. Scatter any extra meat filling around the peppers in your pan.
Sprinkle each pepper half with two tablespoons of shredded mozzarella. Gently pat the cheese onto the peppers.
Bake, uncovered, for 15 minutes at 375 degrees F. Then, broil the peppers for two minutes to brown the cheese, if desired.
While the peppers are baking, gently rinse your basil leaves and pat them dry. Stack a few leaves, roll them up, and slice them into ribbons. When the stuffed peppers are done, sprinkle the basil on top and serve with extra marinara sauce. Refrigerate leftovers for up to four days.
Recipe time does not include making the marinara sauce or rice. I recommend making these stuffed peppers when you have leftover rice and sauce; otherwise, add 20 minutes to the recipe time.