Preheat oven to 350 degrees, grease a 9x13 casserole dish.
Brown and crumble ground beef and onion together until beef is fully cooked and no longer pink. Drain grease if needed.
To the beef and onions add: minced garlic, crushed tomatoes, water, basil, 1 tsp oregano, thyme, crushed pepper flakes, salt and pepper.
Simmer for 15-20 minutes.
In a large bowl whisk together milk and eggs.
Add 1 tbsp oregano, 1 cup mozzarella, ½ cup Parmesan, salt and pepper.
Fold in cooked spaghetti noodles.
Spread the noodle mix evenly in the 9x13 dish.
Top noodles with the sauce. Top sauce with the remaining cup of mozzarella and ½ cup Parmesan cheeses.
Bake uncovered for 30-40 minutes, and golden brown and bubbly.
Let rest for at least 10 minutes before serving.