Preheat oven to 350 degrees F. Spray a 13x9-inch baking pan with cooking spray; set aside. Cook manicotti 9 minutes, or according to package directions; rinse with cold water and drain.
Heat oil in a large skillet over medium heat. Add onion, tomato, green pepper ,and garlic; cook 5 minutes, stirring often, or until vegetables are softened.
In a large bowl, mix vegetables, chicken, Mozzarella, Ricotta, egg, 1/2 cup Parmesan, basil, salt, and pepper until mixed. Using a small spoon, fill each manicotti with about 1/2 cup mixture.
Pour 1/2 of the marinara sauce into prepared baking pan. Arrange filled manicotti over sauce and top with remaining sauce. Sprinkle with remaining Parmesan. Bake, uncovered, for 30 minutes or until manicotti is heated through and sauce is bubbling.