1) Cube eggplans and drizzle 2 Tbsp. of olive oil in a large skillet (the largest you have) and get your eggplant started. Let it cook until well-browned over medium-high heat (6-8 minutes) and then transfer to a paper towel to drain.
2) In the same skillet, add another 2 tablespoons of oil and add your onions and garlic. Cook for a few minutes until the onions get soft, probably 3 minutes. Then add your cinnamon, cloves, and red pepper flakes if you are using them.
3) Add your tomatoes and let it reduce and get pretty thick. Then add your eggplant and you will end up with a ragu basically.
4) Cook all pastas according to package. Try not to overcook them.
5) Toss this miscellany with two tablespoons of butter and 2 tablespoons of breadcrumbs and set it aside.
6) Start cheese sauce by making a basic roux. Melt 4 tablespoons of butter in a saucepan and slowly whisk in 4 tablespoons of flour. Cook it slowly until it starts to turn a medium brown color.
7) Slowly whisk in milk until it is all combined and you have a creamy sauce. Almost gravy like. If it isn’t quite thick just let it simmer for a minute or two. It will thicken up.
8) Slowly drizzle a bit of your hot milk mixture into your eggs. Again whisking quickly. This will bring your eggs slowly up to temperature but it won’t cook them.
9) Once you’ve added a cup of your milk mixture into your eggs and it is still liquid, you can then safely pour your eggs into your milk mixture and it should be alright. You might get a few lumps, but that’s okay.
10) Then add 1.5 cups Parmesan and your fresh nutmeg into this mixture.
11) In a 9×13 baking dish, add Pasta. Veggie sauce. Pasta. Veggie Sauce. Cheese sauce. Sprinkle with extra Parm and breadcrumbs.
12) Bake this at 350 for 45 minutes and then let it cool for at least 5 minutes before you eat it.