Baked Pasta with Tomatoes & Eggplant

In a medium pot or Dutch oven set over medium heat, warm 1/2 cup oil. Add the eggplant and sauté until tender, stirring frequently, about 5 minutes. If the eggplant sticks to the pot, add a little more oil.
Add 2 tablespoons more oil to the pot along with the onions and fennel, and cook, stirring occasionally, until the onion is tender but not browned, 6 to 8 minutes. Add the garlic and cook, stirring often, for 1 minute. Stir in the chicken stock, crushed tomatoes, fennel seeds, oregano, thyme, red pepper flakes, 1 tablespoon salt, and 2 teaspoons black pepper.
Pour the can of whole tomatoes, including the liquid, into a food processor and pulse until the tomatoes are coarsely chopped. Add the tomatoes and the liquid to the pot. Bring to a boil,reduce the heat to medium-low, and simmer, uncovered, for 15 minutes, stirring occasionally. Taste and adjust seasonings if necessary.

Preheat the oven to 500°F (260°C). Place three 6-inch (15-cm) gratin dishes or a 1-quart baking dish on a rimmed baking sheet.
Bring a large pot of water to a boil, add 1 tablespoon salt, and stir in the pasta. If you’re using a single type of pasta, cook it for 1 to 2 minutes less than the directions on the package. If you’re using both kinds of pasta, start with the one that cooks longest and add the second later so they finish at the same time. You want the pasta to be quite al dente (as in, not fully cooked) as it will continue to soften while the casserole bakes. Drain the pasta.
Pour the soup into a large bowl, add the cooked pasta, the mozzarella, 2 tablespoons Parmesan, 1 1/2 teaspoons salt, and 3/4 teaspoon pepper and toss well.
Divide the mixture evenly among the gratin dishes or pile it all into the baking dish, dot the tops with butter, and bake until hot and bubbly and the pasta begins to brown, about 10 minutes. Sprinkle each dish with the remaining Parmesan, bake for another 4 minutes, and serve hot.