Make the marinara sauce first by heating oil over medium heat. Add the garlic cloves and chili flakes and allow to infuse the oil for 2 - 3 minutes. Add the diced tomatoes, tomato paste, sea salt, pepper, and fresh basil and mix well. Turn the heat down to low and allow 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 and then flip over to sprinkle the other side. Allow to sit for 30 minutes before drying off excess water with a paper towel.
Preheat your oven to 400F (200°C) and line a baking tray with baking paper.
In a medium mixing bowl, whisk together the almond flour, oregano, parsley, and thyme. Set aside. In another bowl whisk together the eggs. Now, take each eggplant round and dip it first into the egg mixture, covering both sides. Then dip it into the almond flour mixture, coating each side well.
Bake the eggplant rounds at 400F for 20 minutes, flipping halfway through. The eggplant rounds should be crispy and golden when done. Once the eggplant rounds have finished cooking, season with salt and pepper and set aside.
Grate the mozzarella and parmesan cheese. Reserve some of the cheese for the top of the eggplant parmesan and you're ready to assemble!
On the bottom of a small casserole dish, lay down a thin layer of marinara sauce. Then add a layer of the crispy eggplant followed by a layer of grated mozzarella and parmesan cheese. Repeat adding marinara sauce, eggplant rounds and cheese until you have run out of ingredients. You should be able to make 2 - 3 layers depending on the size of your casserole dish.
Once you have layered all your ingredients, place sliced mozzarella rounds over the tops of the eggplants and cover with the reserved mozzarella and parmesan cheese. Bake until the cheese is melted and bubbling which takes about 35 - 45 minutes.
Allow the eggplant parmesan to cool slightly and then slice and serve.