Preheat oven to 400˚F.
Brush prepared pepper halves with 2 Tbsp olive oil, then sprinkle with 1/2 tsp salt, 1/2 tsp black pepper, and 1/2 tsp garlic powder. Place peppers on a baking sheet, then roast for 15 to 20 minutes.
In a large skillet over medium high heat, heat 1 Tbsp oil. Once hot, add onion and pepper, cooking until softened, about 5 minutes, stirring occasioanlly.
Stir in garlic and cook for 30 seconds to 1 minute until fragrant. Stir in tomatoes, and cook, stirring occasionally, for about 3 minutes. Stir in beef, breaking it apart with a wooden spoon, until browned, about 5 minutes.
Stir in Italian seasoning and red pepper flakes. Add marinara sauce, stirring to combine, and cook for another 5 to 6 minutes.
Remove peppers from the oven and place in a large casserole dish. Fill each pepper half with the beef mixture, filling to the top. Cover the peppers evenly with cheese and bake for another 15 minutes.
Garnish with freshly chopped basil and serve immediately.