Prepare the eggplants: Preheat oven to 375°F (190°C). Score the flesh of each eggplant half and brush with olive oil, sprinkle with salt and pepper. Roast for 20 minutes until slightly softened.
Prepare chicken filling: In a skillet, sauté onion and garlic until translucent. Stir in shredded chicken, marinara, Italian seasoning, red pepper flakes, Parmesan, and mozzarella. Cook for 5 minutes until combined and heated through.
Stuff the eggplants: Scoop a little flesh out of the roasted eggplants to make space for the filling. Fill each half with the chicken mixture.
Top with cheese: Sprinkle remaining mozzarella and Parmesan over stuffed eggplants.
Bake: Return to oven and bake for 15–20 minutes until cheese is melted and golden.
Garnish and serve: Remove from oven and garnish with fresh basil leaves. Serve warm.