Preheat the oven to 200 degrees. Toast the ricotta on a baking sheet until golden on all sides, about 15 minutes. Allow the cheese to cool, then grate it on a large hole grater and set aside.
To make the sauce, place 3 tablespoons of the extra virgin olive oil in a skillet over medium heat and saute the onion for 4 minutes or until soft. Add the garlic and red pepper flakes and saute for 3 more minutes. Add the tomatoes and allow to simmer over low heat for 20 minutes. Puree the sauce, stir in the basil and reserve.
Trim the bottoms and tops off the eggplants then cut them lengthwise into 1/4-inch thick slices. Lightly salt the eggplant and place it in a colander with a bowl on top to press it down. Allow to stand for 30 minutes. Place pure olive oil to a depth of 1/4-inch in a heavy-bottomed pot over medium heat. Fry the eggplant until golden brown on both sides, turning once. Drain well on paper towels and season with fresh pepper.
Heat the oven to 350 degrees. Cook the penne al dente. Drain the pasta well, toss it with three-fourths of the sauce and half the cheese. Place a layer of the pasta in a 9 by 13-inch baking dish, covering it with a layer of fried eggplant. Layer the remaining pasta on top and then the remaining eggplant on top of that. Sprinkle the eggplant with the remaining cheese, drizzle with the remaining sauce and one tablespoon of olive oil. Bake in the oven for 5 minutes, then serve.