Bring a large pot of water to boil. Add pasta and cook until pasta is tender but slightly undercooked (about 3 minutes less than the package recommends) as pasta will continue to cook during the baking process.
Meanwhile, in a medium pan cook sauce and red pepper flakes until warm; add spinach, carrots and cream cheese. Cook, stirring, over low heat until spinach wilts and cheese melts.
Drain pasta and place in an 8x8 inch baking dish. Pour tomato sauce over ziti; toss gently to mix. Sprinkle with mozzarella cheese.