In a medium pot, heat the olive oil over medium heat. Add the minced garlic and chili flakes and cook for 2 – 3 minutes.
Add the diced tomatoes, tomato paste, sea salt, pepper, and fresh basil. Mix well, then turn the heat down to low and allow the marinara to simmer for 20 – 30 minutes.
Slice the eggplant into 1/4 inch thick rounds and place on a baking tray. Sprinkle sea salt over the top side of the eggplant, then flip over to sprinkle the other side. Allow to sit for 30 minutes, then dry off excess water with a paper towel.
Preheat your oven to 400F (200°C) and line a baking tray with parchment paper.
In a medium mixing bowl, whisk together the almond flour, oregano, parsley, and thyme. Set aside. In a separate bowl, whisk together the eggs.
One at a time, dip an eggplant round first into the egg mixture to cover both sides, then into the almond flour mixture. Make sure each side is well-coated with the almond flour and herb mix, then set onto the baking tray lined with parchment paper.
Repeat until all eggplant rounds are coated.
Bake the eggplant rounds at 400F for 20 minutes, flipping halfway through, until they’re crispy and golden. Remove from the oven, season with salt and pepper, and set aside.
Grate the mozzarella and parmesan cheese, setting aside some for the top of the casserole.
Spread a thin layer of marinara sauce on the bottom of a casserole dish. Add a layer of the crispy eggplant rounds, then cover with a layer of grated mozzarella and parmesan cheese.
Repeat the layering until you have used all the eggplant rounds. You should have 2 – 3 layers, depending on the size of your casserole dish.
Top with mozzarella slices and reserved mozzarella and parmesan.
Bake for 35-45 minutes at 400F (200°C) until the cheese is melted and bubbling. Remove from the oven and allow to cool slightly before serving.