Position oven rack in center; preheat to 425°F. Lightly coat a 9-by-13-inch broiler-safe baking dish with cooking spray. Combine pasta, tomatoes, water, spinach, onion, basil, tomato-and-basil seasoning, Italian seasoning, garlic powder, pepper and crushed red pepper in the prepared baking dish; toss to mix well, making sure the pasta is submerged in the liquid.
Cover with foil and bake for 20 minutes. Remove from the oven; stir the mixture. (This will ensure the pasta cooks evenly.) Re-cover with the foil. Bake for 10 minutes. Stir, sprinkle with cheese and dot with pepperoni. Cover and bake until the pasta is tender, about 15 minutes more.
Remove the foil (without removing the baking dish from the oven) and bake until the cheese is golden brown in spots, about 5 minutes. Let stand for 10 minutes before serving.
