Arrange pepper halves in a 9 inch square glass baking dish. Cover dish with plastic wrap. Poke a few holes in the plastic wrap for vents, and heat 4 minutes in the microwave, or until tender.
In a medium bowl, mix tomatoes and their liquid, rice, and water. Cover with plastic, and cook in the microwave for 4 minutes, or until rice is cooked.
Stir green onions, corn, kidney beans, and red pepper flakes into the tomato mixture. Heat in the microwave for 3 minutes, or until heated through.
Spoon hot tomato mixture evenly into pepper halves, and cover with plastic wrap. Poke a few holes in the plastic to vent steam, and heat in the microwave 4 minutes. Remove plastic, sprinkle with mozzarella cheese and Parmesan cheese, and allow to stand 1 to 2 minutes before serving.