MAKE THE TOMATO SAUCE:
Combine onion, garlic, basil, red pepper flakes, and olive oil in a large, heavy pot with a lid. Simmer for five minutes over medium heat, stirring, and then add the crushed tomato. Season with salt and pepper and let simmer for about 30 – 40 minutes with the lid on but allowing about ¼-inch to allow steam to escape. It should be flavorful and thickened. Set aside until you’re ready to layer it with the eggplant. The sauce is best when it’s made in advance.
PREPARE THE EGGPLANT:
Peel the eggplant and slice off and discard the 2 ends of each. Slice the eggplant lengthwise evenly into ¼ to ½ – inch slices, salt both sides, then let them sit for 20 minutes. This draws out the moisture. After 20 minutes, rinse, and then pat dry with a kitchen towel.
In a large skillet, heat about half-inch of oil. Dredge each eggplant slice in the flour, coating both sides and shaking off the excess. Fry the slices in batches, a couple of minutes on each side, until golden. Remove slices to a plate while you fry the rest of the batches.
PREPARE THE EGGPLANT PARMESAN:
Preheat the oven to 400°F. In the bottom of a large baking pan or dish, spread one ladleful of Tomato Sauce to cover the bottom. Layer, overlapping, half of the eggplant slices on top of the sauce.
Ladle on half of the remaining Tomato Sauce, spreading to cover the eggplant slices evenly. Sprinkle on half of the grated Parmesan cheese then layer on half of the mozzarella to cover.
Repeat with the rest of the eggplant slices, then the rest of the sauce, the rest of the parmesan and finally cover it all with the remaining mozzarella.
Bake in the preheated oven for 20–30 minutes until the cheese is bubbling and golden.