Start water boiling for the pasta. Preheat oven to 375degF.
In a frying pan over medium-high heat, add bacon, onions, garlic, Italian seasoning, and red pepper flakes. Cook until bacon is crispy. Drain off excess grease. Reduce heat to medium low and add crushed tomatoes and let simmer.
Add pasta to boiling water and cook for 9 minutes (it will not be fully cooked). Drain in colander and return to pot.
Stir parmesan cheese into red sauce and pour over pasta. Toss to coat. Divide pasta up into baking dishes. Sprinkle each with mozzarella cheese and then crushed croutons. Bake for 20 minutes.
*If you don't have individual baking dishes, you can use a 13x9 baking dish, just increase bake time to 30 minutes.